So you just dropped 6 years of emulation work and updates....not a clever decision if you ask me. Again, there is NO need to use an old MAME editiion.
Yes, of course the scanner alters the sets....you didn't spot the fix option checkboxes?
Why the scanner do things the rebuidler doesn't do? Well, I guess you have a major wrong assumption here.
I don't know where you got the idea that the rebuilder is what you need. The rebuilder is a file-by-file stupid check checksum and recreate matched files in the destination. It is useful if you got a bunch of messy folders and want to see what is valid from the this big amount of junk. Nothing more. A plain add-files-from-a-source-to-destination.
Again, the scanner is the main module. The one to use to update your collection.
And again, there's nothing confusing.
- Profiler->Create->use the latest MAME binary (this has to be done only once)
- Settings->Setup rompaths (Samplepaths, if you like) (this has to be done only once)
- Scanner-> choose prefered merge mode, enable all fix options, scan, after that you have a clean collection (but of couse there might be missing files). They can be added either via Scanner fix-missing or the rebuilder.
And when MAME udpates you simply start with the scanner (since loading the profile automatically detects the MAME change and updates the profile).
If you did not do a tutorial yet, you should read one. If you already read one and it claimed that the rebuilder is the one to use, it was a wrong one.