I can confirm that this issue exists and the workaround works perfect.
Currently migrating from CM12 to 1511 and we did some cleanup of categories before starting the migration...
Did a somewhat ugly hack to find all ID's from the logfile...
$instanceIDs = @()
$logFilePath = "C:\Program Files\Microsoft Configuration Manager\Logs\migmctrl.log"
Get-Content -Path $logFilePath | ForEach-Object {
$s = $_
if ($s -like "*Couldn't find the specified instance SMS_CategoryInstance.CategoryInstance_UniqueID='DriverCategories:*") {
$s = $s.Trim() + "'~~"
$s = $s.Substring($s.IndexOf("CategoryInstance_UniqueID='DriverCategories:") + 45)
$s = $s.Substring(0, $s.IndexOf("'"))
$instanceIDs += $s
}
}
$instanceIDs | Sort-Object -Unique