How to properly merge two projects, when one of them was derived from the other, which results in several conflicting assets?

I think many of us have been in this state and this question has been asked before to no avail, so here's the issue:

Two projects, A and B. Project B was initially a copy of project A and a ton of changes have been made. The main scene of project B has to be imported in a new version of project A, let's call it A2. Unfortunately, even if you rename and move all the assets into a different folder and export the scene you need, many items have kept their original IDs, so when you import back to project A2 they will try to overwrite their old cousins, ignoring the different directory tree and name. I'm mostly talking about 3D assets, materials, textures and scenes/scene layouts which have all been edited (scripts are a different matter so let's assume they do not exist for the moment, for the sake of simplifying the issue).

I know that one method for tackling this is making a copy of every single asset that is derived from A and has been reused and altered in B, then substituting the original with the copy inside the scene(s) you want to transfer/export. You can see how this can easily become a nightmare, especially on larger projects.

Does anybody have any idea of another way to manage this? Maybe there's a script or another way to mass-change the UUIDs all over a project?