That sounds wrong (if I fully understand it), you're saying that the scanner adds files to unselected sets? How? By fix-missing? If a set is disabled it should not even complain about missing files nor should a fix-missing operation work on it. In full merged sets you may run into weird effects if you e.g. enabled a clone but got the parent disabled, then of course the "parent" set exists but only with the clone files....Disabling sets is a bad idea anyhow ;-)
The way you described it, now I'm able to articulate the issue better. If I only want sets that are not preliminary, I run into issues where the parent is disabled and the clone is enabled. My work around is to enable "parents, clones, devices, bios" which works great and is my way of dealing with MAME's ever growing list of sets stuck in the forever preliminary phase. Also, I only use split sets. Again, I'm perfectly fine with this solution and if this can be carried over to the new software, it would be great. Also, would No-Intro dats be impacted in the future?