This script checks for invalid books in the calibre library by looking for empty covers and then searches for the original book file in the downloads folder

downloadBooks.ps1

Set-Location C:\CalibrePortable\Calibre\
$calibreNS = @{ 'dc' = 'http://purl.org/dc/elements/1.1/'
    'calibre'        = 'http://calibre.kovidgoyal.net/2009/metadata' 
}
$formatLessBookIds = [int[]](&.\calibredb.exe search 'formats:false and (identifiers:"=isbn:")' --library-path="..\Calibre Library\" | ForEach-Object { $_ -split ',' })
$formatLessBooks = Import-Clixml -Path .\formatLessBooks.xml
if($null -eq $formatLessBooks -or $null -eq $formatLessBooks.Hash -or $formatLessBooks.Hash -ne $formatLessBookIds.GetHashCode())
{
    $formatLessBooks = @{ Hash = ($formatLessBookIds.GetHashCode());Books = ($formatLessBookIds | ForEach-Object { [xml](&.\calibredb.exe show_metadata --as-opf $PSItem --library-path="..\Calibre Library\") } | Where-Object { [string]::IsNullOrWhiteSpace((&.\calibredb.exe search formats:true title:`"$(Select-Xml -Xml $PSItem -Namespace $calibreNS -XPath '//dc:title' | ForEach-Object { $_.Node.InnerXml })`" author:`"$((Select-Xml -Xml $PSItem -Namespace $calibreNS -XPath '//dc:creator' | ForEach-Object { $_.Node.InnerXml }) -join ' & ')`" --library-path="..\Calibre Library\" 2>$null | ForEach-Object { $_ -split ',' } ))})}
    Export-Clixml -InputObject $formatLessBooks -Path .\formatLessBooks.xml
}
$mutex = New-Object System.Threading.Mutex -ArgumentList @($false, 'calibre-portable-update-metadata')
$formatLessBooks.Books | ForEach-Object -ThrottleLimit 16 -Parallel {
    $mutex = $using:mutex
    $calibreNS = $using:calibreNS
    Set-Location C:\CalibrePortable\Calibre\
    $title = Select-Xml -Xml $PSItem -Namespace $calibreNS -XPath '//dc:title' | ForEach-Object { $_.Node.InnerXml }
    $isbn = Select-Xml -Xml $PSItem -Namespace $calibreNS -XPath '//dc:identifier' | Where-Object -FilterScript { $_.Node.scheme -eq 'ISBN' } | ForEach-Object { $_.Node.'#text' }
    $id = Select-Xml -Xml $PSItem -Namespace $calibreNS -XPath '//dc:identifier' | Where-Object -FilterScript { $_.Node.scheme -eq 'Calibre' } | ForEach-Object { $_.Node.'#text' }
    if (-not [String]::IsNullOrWhiteSpace( $isbn ) -and -not  [String]::IsNullOrWhiteSpace( $id ))
    {
        $sleepTime = 3
        $uri = "http://libgen.is/search.php?req=$isbn&open=0&res=25&view=simple&phrase=1&column=identifier&sort=year&sortmode=DESC"
        $request = Invoke-WebRequest -Uri $uri 2>$null
        while ($request.StatusCode -ne 200)
        {
            Start-Sleep -Seconds ($sleepTime *= 2)
            $request = Invoke-WebRequest -Uri $uri 2>$null
        }
        Get-Package -Name 'AngleSharp' | ForEach-Object { Split-Path $_.Source } | Get-ChildItem -Filter '*.dll' -Recurse | Where-Object { $_ -Like '*standard*' } | Select-Object -Last 1 | ForEach-Object { Add-Type -Path $_ -ErrorAction SilentlyContinue -Verbose }
        $parser = [AngleSharp.Html.Parser.HtmlParser]::new()
        $parsedContent = $parser.ParseDocument($request.Content)
        $formats = New-Object -TypeName 'System.Collections.Generic.HashSet[string]'
        $parsedContent.QuerySelectorAll('body > table.c > tbody > tr') | Select-Object -Skip 1 | ForEach-Object {
            $format = $_.QuerySelector('td:nth-child(9)').InnerHtml
            if (-not([String]::IsNullOrWhiteSpace($format)) -and $formats.Add($format))
            {
                $requestDL = Invoke-WebRequest -Uri ($_.QuerySelector('td:nth-child(10) > a').GetAttribute('href'))
                $parsedDLContent = $parser.ParseDocument($requestDL.Content)
                $uri = [uri]::new(($parsedDLContent.QuerySelector('#download > h2 > a').href))
                $md5 = $uri.segments[3] -replace '/', ''
                $filename = Join-Path $env:TEMP "$id.$($uri.segments[-1] -split '\.' | Select-Object -Last 1 )"
                if (-not(Test-Path $filename -PathType Leaf) -or ($md5.ToUpperInvariant() -ne (Get-FileHash -Path $filename -Algorithm MD5).Hash))
                {
                    $request = Invoke-WebRequest -Uri $uri -OutFile $filename -Resume  2>$null
                    while ($request.StatusCode -ne 200)
                    {
                        Start-Sleep -Seconds ($sleepTime *= 2)
                        $request = Invoke-WebRequest -Uri $uri -OutFile $filename -Resume  2>$null
                    }
                }
                try {
                    $mutex.WaitOne() | Out-Null
                    $ebookFile = Get-Item $filename
                    &.\calibredb.exe add_format $id "$ebookFile" --library-path="..\Calibre Library\"
                    @{Id=$id; Ebook=$ebookFile; Title=$title; Filename=$filename} | Format-Table -AutoSize -Wrap | Write-Output 
                } finally {
                    $mutex.ReleaseMutex() | Out-Null
                }
            }
        }

    }
    
}

fixBrokenBooks.ps1

$calibreLibraryPath = "$env:USERPROFILE\Calibre Library"
#Install pre-requisite module Communary.PASM for approximate string matching if necessary
#See https://github.com/gravejester/Communary.PASM/tree/6fe3b5ea01e8f49aeccbde0db0dc777079b9e9cd
if (-not (Get-Module -ListAvailable -Name Communary.PASM)) {
	$m="Installing missing approximate string matching module Communary.PASM"
	Write-Host $m
	Write-Log -Message $m -Level "WARN" -logfile $log
	# Check to see if we are currently running "as Administrator"
	if ($myWindowsPrincipal.IsInRole($adminRole))

	   {
		   # We are running "as Administrator" - so change the title and background color to indicate this
		   $Host.UI.RawUI.WindowTitle = $myInvocation.MyCommand.Definition + "(Elevated)"
		   $Host.UI.RawUI.BackgroundColor = "DarkBlue"
		   clear-host
		   Install-Module Communary.PASM
	   }

	else
	   {
		   # We are not running "as Administrator" - so relaunch as administrator   

		   # Create a new process object that starts PowerShell
		   $newProcess = new-object System.Diagnostics.ProcessStartInfo "PowerShell";   

		   # Specify the current script path and name as a parameter
		   $newProcess.Arguments = $myInvocation.MyCommand.Definition;   

		   # Indicate that the process should be elevated
		   $newProcess.Verb = "runas";   

		   # Start the new process
		   [System.Diagnostics.Process]::Start($newProcess);   

		   # Exit from the current, unelevated, process
		   # exit
	   } 
}
#Install pre-requisite pdfinfo by XpdfReader if necessary
#See https://www.xpdfreader.com/pdfinfo-man.html
if (-not (where.exe pdfinfo.exe)){
	$m="Installing missing pdfinfo program by XpdfReader"
	Write-Host $m
	Write-Log -Message $m -Level "WARN" -logfile $log
	$pdfinfoZipDl = $($(iwr -Uri 'https://www.xpdfreader.com/download.html' -Method Get).ParsedHtml.links | foreach {$_.href | Select-String -Pattern 'xpdf-tools-win.*\.zip$' }).ToString()
	(New-Object Net.WebClient).DownloadFile($pdfinfoZipDl,"$env:TEMP\xpdf-tools-win.zip");(new-object -com shell.application).namespace('"$env:TEMP').CopyHere((new-object -com shell.application).namespace("$env:TEMP\xpdf-tools-win.zip").Items(),16)
	$pdfInfoLoc = "$env:TEMP\" +  $(Get-ChildItem -Path $env:TEMP -Name "xpdf-tools-win*" -Directory) + "\bin64\pdfinfo.exe"
}
else {
	$pdfInfoLoc = where.exe pdfinfo.exe;
}
$log = New-TemporaryFile
Function Write-Log {
    [CmdletBinding()]
    Param(   
    [Parameter(Mandatory=$True)]
    [string]
    $Message,
	[Parameter(Mandatory=$False)]
    [ValidateSet("INFO","WARN","ERROR","FATAL","DEBUG")]
    [String]
    $Level = "INFO",

    [Parameter(Mandatory=$False)]
    [string]
    $logfile
    )

    $Stamp = (Get-Date).toString("yyyy/MM/dd HH:mm:ss")
    $Line = "$Stamp`t$Level`t$Message"
    If($logfile) {
        Add-Content $logfile -Value $Line
    }
    Else {
        Write-Output $Line
    }
}
$confidence = 0.90
$calibreNS = @{ "dc" = "http://purl.org/dc/elements/1.1/"; "calibre" = "http://calibre.kovidgoyal.net/2009/metadata" };
$webNS = @{'xmlns'="http://www.w3.org/1999/xhtml"}
$files = Get-ChildItem -Path $env:USERPROFILE\Downloads -Recurse -File -Include *.AZW, *.AZW3, *.AZW4, *.CBZ, *.CBR, *.CBC, *.CHM, *.DJVU, *.DOCX, *.EPUB, *.FB2, *.FBZ, *.HTML, *.HTMLZ, *.LIT, *.LRF, *.MOBI, *.ODT, *.PDF, *.PRC, *.PDB, *.PML, *.RB, *.RTF, *.SNB, *.TCR, *.TXT, *.TXTZ                  ; #has $files.Count many elements
$ids = ([string](calibredb search cover:False)).Split(",");
$candidates = New-Object 'System.Collections.Generic.Dictionary[Float,System.IO.FileSystemInfo]'
foreach ($id in $ids) {
	Write-Progress -Activity "Trying to find good copies of broken books" -Status "$([int16]$(100*$ids.IndexOf($id)/$ids.Count))% Complete:" -PercentComplete (100*$ids.IndexOf($id)/$ids.Count);
	$err = New-TemporaryFile
	$out = New-TemporaryFile
	$calibreBookFilename = Get-ChildItem -Path $calibreLibraryPath -Include "*($id)" -Recurse
	$book = [xml](calibredb.exe show_metadata --as-opf $id)
	$author = Select-Xml -Xml $book -Namespace $calibreNS -XPath "//dc:creator" | ForEach-Object { $_.Node.Innerxml }
	$title = Select-Xml -Xml $book -Namespace $calibreNS -XPath "//dc:title" | ForEach-Object { $_.Node.Innerxml }
	$compositeName = $($(if($title.Equals("untitled")){$calibreBookFilename.Name}else{"- $author"}) + $(if($author.Equals("Unknown")){""}else{"- $author"}))
	#if($title -ieq 'untitled' -and $author -ieq 'Unknown' -and $calibreBookFilename.Name -ieq 'untitled - Unknown') 
	#{	
		foreach ($file in $files) {
			Write-Progress -Activity "Looking for $title by $author" -Status "$([int16]$(100*$files.IndexOf($file)/$files.Count))% Complete:" -PercentComplete (100*$files.IndexOf($file)/$files.Count);
			$compar = 1 - $(Get-JaccardDistance  -a $compositeName -b $file.Name.Split(".")[0] -CaseSensitive)
			if ($file.Name.Split(".")[0] -gt 0) {
				try{
					$candidates.Add($compar,$file) | Out-Null
				}
				catch [ArgumentException]{
				   $m="'" + $file.Name.Split('.')[0] + "' had the same confidence as '" + $candidates[$compar].Name.Split('.')[0] + "'"
				   #Write-Host $m
				   Write-Log -Message $m -Level "DEBUG" -logfile $log
				}
				if (-not $candidates.GetEnumerator().Value -ceq $null -and $compar -ge (1-$confidence)) {
					Write-Progress -Activity "Looking for $title by $author" -Status "Found $($replacement.Name) at $compar% confidence" -PercentComplete 100
					Clear-Variable compar
					break
				}
			}
		} 
		$m="Looking for $title by $author" 
		Write-Host $m 
		Write-Log -Message $m -Level "INFO" -logfile $log
		$bestGuess = $(($candidates.GetEnumerator() | sort -Property Key))[0]
		$compar = $bestGuess.Key
		$replacement = $bestGuess.Value;
		$m="Found $($replacement.Name) at $compar% confidence"
		Write-Host $m  -NoNewLine -ForegroundColor DarkGreen
		Write-Log -Message $m -Level "INFO" -logfile $log
		if($compar -lt (1-$confidence)){
			$m=" having low confidence `($compar`)"
			Write-Host	$m -ForegroundColor DarkYellow
			Write-Log -Message $m -Level "INFO" -logfile $log
		}
		Start-Process -FilePath $pdfInfoLoc -ArgumentList "-meta `"$($replacement.FullName)`"" -NoNewWindow -RedirectStandardError $err -RedirectStandardOutput $out
		if ( $(Select-String -InputObject $err -Pattern "(Error|Warning)") -ceq $null -and -not ($(Get-Content $out) -ceq $null)) {
			$m="`nReplacing old file with new one" 
			Write-Host $m -ForegroundColor Green
			Write-Log -Message $m -Level "INFO" -logfile $log
			Write-Host $out -ForegroundColor Green
			Write-Log("INFO",$out,$log)
			calibredb add_format $id "$($replacement.FullName)"
		} else {
			$m="`nThe file $($replacement.FullName) was corrupt.`nNo valid file found for $title by $author.`nRemoving book with ID $id from Calibre"
			Write-Host $m  -ForegroundColor DarkRed -BackgroundColor Black
			Write-Log -Message $m -Level "WARN" -logfile $log
			calibredb.exe remove $id
		}
	#} 
	#else {
		#$m="`nThe book with ID $id was corrupt, had no title or author. Its filename is $($calibreBookFilename.Name). It is thus impossible to replace.`nRemoving book with ID $id from Calibre"
		#Write-Host $m  -ForegroundColor DarkRed -BackgroundColor Black
		#Write-Log -Message $m -Level "INFO" -logfile $log
		#calibredb.exe remove $id
	#}
	Remove-Item $out, $err -Force
	Clear-Variable candidates, err, out
	$candidates = New-Object 'System.Collections.Generic.Dictionary[Float,System.IO.FileSystemInfo]'
}