hmm..ok...there are two things...
zip, rar, most likely 7z as well, can store folders directly (folder slash encoded in the name) and some archive tools add another folder entry in the archive. For zip files these are not needed and cmpro's compressor general options offer a switch to mark them as deleted. They can be removed without doing any harm.
Now with that rar file, this detection failed...which I quickly fixed...but correctly detects the obsolete entry (depending on that compressor switch) but when removing it, cmpro constructs a delete operation which looks like
winrar "d -y -ibck -m5 -s- E:\temp\test\001-421.rar 001-421"
and it seems that winrar does not remove the single folder entry but the whole folder including all files....
so it seems that this functionality should be disabled for rar files completely...unless I find maybe a different switch to remove only the 'dummy' folder entry...
so turning off the cmpro option in compressor settings won't help you at the moment since the check is not working correctly for rar files....over the weekend I will post an update...