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It would have been better to delete the files from within PSA SE - that keeps everything in step. You can delete the thumbs with DEL or are you asking how to identify the deleted files?
Yes, how can I identify the deleted files?
Or how can I update my catalog, so PSA only show the files that are actualy on my harddrive?
You could start your catalog afresh, but that would lose any tagging you have done. Would that be a problem for you?
that would be a big problem :-)
There is no ideal solution, but this might be good enough for you:
Select all the pictures in PSA SE - CTRL/A.
Do F11 and cancel out of the "searching" dialog.
You should now see a little red marker on each picture that was not found. Select each of these [with click then CTRL/click] and then delete them [DEL].