The only way I can think of for this to happen is you have two computers opening the same .por file. On one computer you have the .user files and on the second one you do not. When you open on the second computer HL would give an error. But if you then saved the characters it could remove reference to the sources.
Other than that I can't think of much. I assume your not doing a Prepare for Distribution on your .por files right? That can change checked sources.
Otherwise I have seen official sources for new books will auto-activate themselves on old characters. But never seen sources get removed.
