Not got much experience with Reaper, have you set the project location? Make sure that you set the paths correctly.
Under preferences (ctrl+p), go to paths. there is a field for default recording path when file isn't saved, or something similar. Set it to something that wont bother you.

I wouldn't rely on this however. Make a new folder for every project you are working on and save within it, then all your files will go there and you wont be searching your entire HD for that one missing file.
use save as, find the old file, select it, and then hit the save button. Reaper will ask you if you want to overwrite, click yes.
Use save as and click on the old file before saving. Not sure why you would want to do this though, best to have (dated) multiple copies in case you make a mistake and need to restore something. You should never be overwriting files.

Also get into the habit of putting all your files on a USB stick after you've finished a session; data doesn't exist unless it's in two places.