OK so I can't find an answer to this anywhere so I apologize if this question has been asked before.

Recently I deleted some files out of my website's root folder that were no longer being used. They were no longer being referenced on any of my website's pages so to try and get rid of some clutter they were deleted. Now whenever I upload my website I get a error/warning telling me these files could not be found and do I want to proceed anyway with the upload. I click proceed anyway and everything uploads just fine but I would love to get rid of the nag screen asking me if I want to proceed. Why does this happen? Is there some way to manually remove the files from the upload list? Many many thanks in advance for any help you guys can provide.
" I love..... Coffee in a cup!!!"

Hello,
Try going to settings> remove files and see if the files that were deleted are listed there, if so remove them, and try and upload again this time using the resync option. This will also change the db file that is on your server.http://kellyinfo.com/comp/comp04.gif

Well i'll be damned, it worked like a charm. Many many thanks!