If the problem occurred at all, then it would have occurred the first time, most likely.

Here's how to check.

First, find one of the corrupted files on your empeg and retransfer it to the empeg from the copy on your computer, this time with the correct settings. If it works, then you know that the copies on your computer are correct. If not, then the copies on your computer are not correct, and you'll have to retrieve them from the initial empeg again.