As some of you are already aware, some CD's have a mastering issue where write offset changes across the disc. For the standardization purpose, I will be calling that "offset shift".
That's an incorrect term. There's only 1 offset per disc, while you're talking about leftovers from earlier burning/dumping mastering stages. Those leftovers are physically present on the disc and need to be kept, since they belong to the disc data.
Here's how that can be handled:
1. Leave transitional sectors intact.
2. Force descramble of all transitional sectors
3. Intelligently detect if the sector is scrambled based on a combination of content criteria and if it is, try to descramble it.
All 3 are wrong, since those leftovers often contain duped data and a plain descrambling will lead to duped sectors. Also, there are quite a lot of cases when those leftovers appear as a part of a first post-data audio track, like http://redump.org/disc/7986/
The main dump should be always left as is, with anything unusual left scrambled.
As for the additional "(Fixed)" dumps we've discussed eariler, you should probably try to descramble all the sectors, but the descrambled sector shouldn't be added into the dump, if exactly the same sector already exists in the descrambled dump (not to be confused with the twin sector-based protections, when there are 2 different sectors with the same headers exist).
There are also cases, when such sector shifts appear in pregap (sectors -150 to -1), so we're loosing a part of vital data for them by not preserving that area - http://redump.org/disc/73334/ as an example. Disc offset (= pregap offset) goes to the "Write offset" in this case and the "new" user area offset goes to the comments. Since we're not preserving the pregap, such discs aren't added as fully scrambled, but it's the only exception, all the other cases should be added as a pair of unfixed + fixed dumps (also, such a pair is a workaround and ideally I would replace them with a pair of scrambled + descrambled dumps).
Whether to fix the ones with garbage data in audio and add as (Fixed) is upto you. If there's a shifted piece of actual audio data in the lead-out area, probably worth to.