and this is a news board not a help board, which is why it's getting off topic. The topic is/was: MAMEUI64 .153 released. Your problem isn't news, but it is appropriate for the programming board.
But yes, you should add "clean" to your build command (or delete your obj folder) each time before you actually build. It prevents a lot of issues such as yours. I'm still not convinced you have a hardware problem. At least not from what you've posted.
Think for a second. If HDD 1 was corrupted and you just copied things to HDD2, do you really think the copied files would 'uncorrupt' themselves when they coppied over? Or that they could even be copied if HDD1 had problems reading? Don't answer here. If you must, start a thread in the PC Hardware board or loony bin (as compiling is no longer the issue).