Because the subject of a has_many relationship, by definition, has only one parent. What you're describing is a many_many relationship. I have a patch that allows Uploadify to work with many_many, but I haven't applied it yet.
Actually, you can probably search the forum and find the patch.
Let me explain. I'm creating an employee object. An employee should have the uppertunity to upload many pictures only attached to the employee object it self. Other employee objects should not have relations to the uploaded pictures. This should be a has_many relationsship for all I know? Or what?
So when the employee opens the multiple upload form and whould like to add more pictures to the existing object it would make sense that the old ones didn't get "deleted" or null'ed.
What you're describing is a has_many. I think you have a problem with your model. What's happening in the block of code you're referring to is that when the page is saved, it destroys all the file relationships and recreates them. The user may have removed files from the list, so every time the page is saved, we rebuild the list.
If you have just added files, then I can't see why you would be having that problem. Can I see your code for the Employee and Photo classes?