If I understand the question correctly, you want to delete the folders on the server but not delete anything locally. You then want to re-add your code using what you have locally. Is that correct?
Possibly the easiest way to do this is to copy the code you have locally into a separate back-up folder on your desktop. Then perform a delete using Source Control Explorer in Visual Studio. Check-in the delete. Finally drag/drop the contents of your local back-up into Source Control Explorer (you need Visual Studio 2008 SP1 for drag/drop to work) so that it adds the appropriate files for you to.
Check the pending adds that you have to make sure all the files you want are included and no files you do not want (i.e. make sure any compilation outputs are not included and that the folder format in source control explorer is how you want it to be)
Once you are happy, check-in your adds.
Let me know if I didn't understand the question correctly.