Update Skype User with New Email Address *Remove the "-whatif" tags to let the actions actually perform.

UpdateSkypeUserWithNewEmail.ps1

Import-Module MSOnline
Write-host "Please enter your Microsoft Office365 Administrative credentials:" -ForegroundColor Cyan
Connect-MsolService -Credential (Get-Credential)
$username = Read-Host "Please enter the users domain username"
$oldemail = Read-Host "please enter the users OLD email address"
$msoluser = get-msoluser -UserPrincipalName $oldemail
$user = get-aduser -identity $username -Properties mail,proxyAddresses
$samaccountname = $user.SamAccountName
$email = $user.mail
$userProxyAddresses = $user.proxyAddresses
$userStatus = $user.Enabled
if ($userStatus -eq "False")
    {
        Write-Host "The user specified is currently disabled, exiting script." -ForegroundColor Red
        exit
    }


Set-ADUser $user -replace @{'msRTCSIP-PrimaryUserAddress' = "SIP:$email"} -whatif
foreach ($proxyaddress in $userProxyAddresses)
            {
                 if (($proxyaddress -like "*sip:*") -or ($proxyaddress -like "*SIP:*"))
                    {
                        Set-ADUser $user -remove @{proxyAddresses="$proxyaddress"} -whatif
                    }
            }

Set-ADUser $user -Add @{proxyAddresses="SIP:$email"} -whatif
Set-MsolUserPrincipalName -NewUserPrincipalName "SMTP:$email" -UserPrincipalName $($msoluser.UserPrincipalName) -whatif