I do not believe this would normally be the case.
I wonder if, when you inadvertently switched to APE, you also inadvertently got the Normalize to 95% before encoding option enabled. That would explain it. Then, the original APE rips themselves would contain the higher gain levels.
If so, the only reasonable way to "fix it" would be to re-rip them. I think, but I'm not sure as I've never enabled or tested that option, that it does not compress dynamic range (it is just "sliding them higher" in the dynamic range scale to "use up" empty space). However, I don't know if it would be a fixed amount per-disc (so keeping the dynamic range consistent between tracks on a particular disc), or if it is per track. If it is consistent within a disc (preserving inter-track range) then you could just ignore it, but I don't know that answer.
In any case, to fix it you'd have to know what precise adjustment it did to reverse it, and it would be way easier to re-rip the discs.