First of all: welcome to the Asylum!

The same disc being part of several box sets happens more and more. As far as the central online database is concerned, the box set with the earliest release date should take precedence, and the disc profile should reflect the characteristics of that set (i.e. release date, cover scans, overview etc.).

So it would seem you're on the right track.

Of course, in your local database you can change the data and add your own cover scans to reflect what you actually have and then lock those data and scans (to prevent them from being overwritten by future updates from the central database), but you can't contribute the changes you made to the central database. In the online display of your collection, the changes you made will be shown, except for the cover scans - these are always drawn from the central database.

Unfortunately, at this point DVD Profiler is unable to properly handle such situations, so it's very much an issue of "first in". This is due to the fact that until now, DVD Profiler has only two ways to identify a profile (within a given Locality, i.e. country of DVD release): UPC and Disc ID. Solutions by adding more (combinations of) profile identifiers have been requested many times in the past, but no such luck so far, I'm afraid.