Hmmmm not sure if the plug-in is custom, might not work. What I have done is to serve files that the user already has a program to view/interact with. So to say, pdf files if you have an acrobat viewer. That works great cause if they don't, they receive the pdf file which they can save and view later on. Of course, if these files should be propietary (and thus not really transferrable to be saved), you've got far more problems than I do
Anyway, the solution proposed should work fine, just modify slightly the act of submitting a file: instead of copy&paste to the server, or ftp it, use an upload php page and update the page at the same time.
You can even add ease of use with 'add new doc' (and then ask for a name) or 'update existing doc' (and then use all the fields you already have, including description etc...). And of course, filtering the file types and everything. In the end, you get much more control.
So, I hope this helps, if you don't see it as a solution, please re-state the details (somehow differently, that is ), and if you're using something else to work that out, please let us know. I am always available to learn new ways to do things
Marc