In our case, there were 45 legacy / lost dlfileentries in our system with no corresponding dlfileversion record. Gather a list of the offending fileEntryIds and use this script to remove them. This script needs to be run before the mass document version cleanup can occur.

lr62-delete-specific-files.groovy

// Delete files that have no dlfileversion record...
// Use this query to find them...:
// select fileEntryId from dlfileentry where fileEntryId NOT IN 
// (select dlfe.fileEntryId from dlfileentry dlfe, dlfileversion dlfv where dlfe.fileEntryId=dlfv.fileEntryId and dlfv.version=dlfe.version);

import com.liferay.portal.model.User;
import com.liferay.portal.service.UserLocalServiceUtil;
import java.util.List;
 
import com.liferay.portal.kernel.repository.model.FileEntry;
import com.liferay.portal.kernel.repository.model.FileVersion;
import com.liferay.portal.kernel.repository.model.Folder;
import com.liferay.portlet.documentlibrary.service.DLAppServiceUtil;
import com.liferay.portlet.documentlibrary.service.DLFileVersionLocalServiceUtil;
import com.liferay.portlet.documentlibrary.model.DLFileVersion;

import com.liferay.portlet.documentlibrary.service.DLFileEntryLocalServiceUtil;
import com.liferay.portlet.documentlibrary.service.DLAppLocalServiceUtil;

previewMode = true;

if(previewMode) {
  out.println(
    """<div class="portlet-msg-alert">Preview mode is on: switch off the flag and execute this script 
    again to make changes to the database</div>""")
}

def SCRIPT_ID = "Delete-Files-w-No-Version"

outputFile = new File(
  """${System.getProperty("liferay.home")}/scripting/out-${SCRIPT_ID}.txt""")

outputFile.getParentFile().mkdirs()

def trace(message) {
  out.println(message)
  outputFile << "${message}\n"
}

try {
	def allfiles = '1302031,1302076,1302081,1325718,1325763,1675804,1840601,1872535,1919354,\
1937807,1937812,1937816,1937946,1938015,1938020,1940276,1940280,1940285,\
2218319,2218324,2218328,2218332,2218336,2218340,2218346,2218350,2218356,\
2218360,2218364,2218370,2218374,2288427,2288452,2288459,2288517,2297297,\
3657858,3721708,5160026,7725031,7725146,8311008,9020340,9020431,9105681';
	String[] filesToWhack = allfiles.split(',')
		for(i=0;i<filesToWhack.size();i++){
		thisFile = filesToWhack[i]
		thisFile = Integer.parseInt(thisFile)
			trace('Deleting: ' + 'fileEntryId=' + thisFile)
				if(!previewMode) {
        			DLAppLocalServiceUtil.deleteFileEntry(thisFile);
				}		
	}
	
} catch (Exception e) {
	println(e)
	e.printStackTrace(out)
}