Okay, the additional ingredient of Dropbox in the other thread might be misleading in the sense that this kind of problem between two projects can be produced using any means to transfer the files from one computer to another. In the case of Dropbox it is using the Internet and a bunch of automatic stuff, but it is essentially the same as copying the files yourself by hand using a drive.
The main issue is to not use this folder sync feature with more than one project. It is designed to be used so you can use other software entirely (most often something mobile, but there are many ways to use it).
That would make sense from the standpoint of it syncing more than it needs to, since modification dates are how it decides whether a file should be synced. However that alone would be fairly “safe” in that even if it syncs unnecessarily, if there is only one project using these files, the content would still be the same in the file.
I can’t say how to avoid the modification date problem—that depends on what did it.
I can say that wouldn’t cause any shuffling by itself. What will cause shuffling is if one project writes out a file as “10 - Name of item .rtf”, and that “40” part is what tells the software which part of the binder it comes from. If another project syncs from this same folder, it might use “40” internally to refer to a completely different file. But it can’t know that, all it sees is a file that should update 40, so the wrong content ends up in the binder.
If you have enough of that going on, it could indeed make a big mess. That shouldn’t happen with text editors that just open files individually, because they don’t care what it is called. The only way you’d get shuffling is if you opened several files and actually cut and paste stuff from one file into another and so on—deliberately you might say.
If you’re saying this is happening and you aren’t using two copies of Scrivener with one sync folder, then the problem is more mysterious. The only thing I can think of that might cause a problem like that is if one duplicates a project on the disk, and they both are using this same sync folder, and one then later on accidentally opens the old one and it syncs—but it’s using old internal numbers and so cannot properly use the newer sync folder. That’s a variation on the “two project problem”, and I’m not certain that would actually happen, but it’s a theory.
What I would recommend for a bit here is to use the File ▸ Back Up ▸ Back Up Now or Back Up To… command before syncing, and turn off the auto-sync on open-close, so that you can better control when it happens, and have the most recent version of the project to return to if it goes wrong. At least until the origin of the problem is discovered. Once things are smoothed out, it can be trusted to go automatic again.