I've encountered what I hope is a rarity, where a title has a different barcode printed on the slip-cover than the one on the cover-art of the keepcase itself.

The title I discovered it for happens to be 2 times present in the online database (once with one barcode and once with the other).
It's the movie 'Now You See Me' as distributed in Belgium:
8713045240165 - barcode on the slip-cover
8713045237721 - barcode on the case insert

Now I was wondering, which barcode has the preference to be entered in the database? I am assuming adding them both is not what should be done normally (as was apparently done for this title).
I would suggest adding the one on the slip-cover because that is the most likely one you scan to enter into your collection.

And secondly, this made me think more about slip-cover and cover-art handling. If a title has a slip-cover you can mark this with a checkbox, but does that marking have any bearing on the cover-art you are supposed to contribute? I mean, do you upload scans of the slip-cover or from the cover of the case (which sometimes is not the same)?

I would like to understand the best practice here.

I am not a moderator, but my first thought is that both are acceptable entries into the system. Especially if they have already been accepted into the system through the review/moderation process. Disc titles in the MyMovies system are barcode dependent, so as long as the barcode is correctly matched to the move title you are ok.

Sometimes discs are sold with the slip cover and sometimes without. alot of people thow out or lose the slip cover, so the disc cover art would be the preferred of the two, it would be up to you which one you want entered into your collection. As long as the slip cover version has the slip cover box checked I would assume that entry is correct. The version without the slip cover with the different barcode, as long as slip cover box is not checked I assume is also correct. The cover scans should also reflect the corresponding with the slip cover being scanned for that version and the case cover art being scanned for the other. I believe that is what the slip cover check box is intended for in the first place.

"The slip cover checkbox should be checked depending on which cover is contributed."

that is interesting information, and I now realise I interpreted it completely differently: I always though that checkbox indicates if a title comes with or without a slipcover, but I always contribute a scan of the case cover (not the slipcover).
I do not remember finding this in the contribution guidelines, so maybe would be good to add this description there.

It does however exposes one problem: some people will prefer to have the slipcover and others the case cover as cover image in their database. And you can only contribute one per title. Maybe we should get some guidance on that as well. Which one is preferred?