Can't overwrite zc files

For some reason, all of a sudden I can't overwrite any files even when changing permissions, and it doesn't matter whether I try through ftp or cpanel. Is there a function in cpanel I can check to see why my zc files are not being overwritten? It's causing major issues in trying to do anything with my store.

(sorry if this is the wrong forum for this, it seemed as good as any for the question :lookaroun)

That sounds like a file ownership problem.

I can see that being an issue when in cpanel for one account and trying to do something for another, because I do have more than account. But for uploading through ftp, wouldn't just logging in as the main ftp user eliminate that problem?