Resolvido isso usando o Windows PowerShell, o cmdlet Clear-Content fez o trabalho:
$dirtostrip = "$strippeddir\backup_$backupdate\$backupdate\alf_data\contentstore"
$files=((dir $dirtostrip -recurse) |?{$_.psiscontainer -eq $false})
for ($i=0;$i -ne $files.count; $i++)
{
if ($files[$i] -eq $null) {continue}
if ($files[$i].length -gt $filesizelimit) {
Clear-Content $files[$i].FullName
}
}