If they were doing conversions manually, I suspect such a major encoding error would have shown up quite quickly. It's bound to cause errors when a file is unopenable in a lot of programs that can't handle non-unicode (heck, Microsoft's own VS code can't handle them).

I doubt even really old NT programs (pre 2000) using UCS-2 would have included unpaired surrogates because IIRC those code points were never mapped to actual characters so I don't think that's an issue in practice.