Ok, I've tried to repeat your ggiana sisters problem. Unfortunately, I can't repeat it. Everytime a removed set appears as fully missing in the next full scan. So I guess, I'd need your old profile *.cmp file (cmpro's settings folder) for your used profile where the problem appears and cmpro.ini.
By the way, on one screenshot you showed a chd naming issue with a sgi_mips chd. This is normal since the new scanner detects a problem when fully merging the sets (same chd file name, different hashes and for decompressed files (and chds are decompressed), you can't have subfolders). The new scanner then adds the sha1 in front of the filename. I can't remember if old cmpro handles this by removing parent/clone relationships of simply ignores it. So getting the wrong name here is normal if you compare old cmpro and new scanner.
Regarding your latest "It finded some bounch (about 50) missing romsets, compared to clrmame scanner." it would be interesting to see what it found.