Revert archived files to specified locations like Downloads, Documents and Desktop
One way to do this is to use a separate user for each project. 

Another way is to not use the standard settings and put all of one project under the same directory. This does mean that you need to treat Downloads as a temporary location, when you download you then move it to a directory you use.

If these do not suit your problem I think you need to expand how things could mess up - also how are they backed up - if you go through this in detail then I think you will see you need to change your working practice