Making backup saves won't do any good with regards to Mental Omega updates. They won't get touched by the update process, so if they stop working it'd be because the mod had moved on and rendered something in the old saves incompatible. Not because they were corrupted. Unless you somehow went back to the old version, the saves wouldn't start working again just because you restored from a backup directory.
Speaking from experience with Twisted Insurrection, small updates (ie bugfixes) don't tend to render saves incompatible. Larger updates however (which, admittedly, is pretty much all Mental Omega updates) tend to shuffle things around as they add new stuff, and that's when things start going wrong. It could be merely cosmetic (e.g. one Twisted Insurrection didn't stop my old saves from working, but if I loaded an old GDI mission save I now had the CABAL and the Nod interface. Another update moved sound pointers around, so that I had Cyborg voice clips playing instead of gunfire sound effects... which given how many rounds got fired and thus how many times that clip played, got annoying quick)... or it could outright refuse to load.
You simply can't tell what will happen until... it happens.
If you know a major update is coming, it's best to finish up halfway done missions before it hits. At least then, if worst comes to worst, the save wasn't wasted.
It's also worth emptying the save directory if they've been rendered non-functional by an update. Just because they've stopped working won't stop them showing up in the Save/Load menu and confusing you.
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