Well, here's an interesting development- don't know if this is actually a thing or not but, I'll mention it anyways.
So I made the cardinal mistake of using a mining laser on Fire 'n' Water, which as you may guess, caused the vanishing bug again. However, in that particular mission I had a couple of Rock Raiders that were not lvl 5 (Or is it 6?). Anyway, all the "trained" guys disappeared as usual (coupled this time with the teleportation out sound very loudly in my left ear), but the untrained rock raiders did not, they hung around working like normal.
As to the trigger that sets this bug off I'm still not fully sure as to what it is, all I know right now that for me laser mining appears to be the culprit, and only on a few levels. But, either I hit a random exception to the rule or the vanishing bug has something to do with the additional upgrade level.