From looking at a few other posts, it is possible to modify the files so that the difference disks will still work.
Do you mean it's possible to doctor the files so that VMware doesn't complain? Yes, I'm sure that is possible but it doesn't mean you've achieved the level of integrity you're looking for. In other words, "work" is very broadly used here.
that the snapshot disks are still valid if I can recreate the snapshot files
Are you planning on substituting one set of .vmsn files with linked disks from different set of changes to a base disk? Good luck!
