When I open my Thesis.tex file I get "File not found"

Worst error description ever!?
This first occured when I opened the .tex file yesterday from my USB. My USB was suddenly write protected (don't know how to fix this either). So I copy the files to a new USB drive (as the files could still be read) but now I have got it again! (This time the USB is not write protected though)
It opens the file just fine and I can still work in it but building the pdf doesn't work (it doesn't finish).
That's the best description I can give.
I think I'm just going to start over copying and pasting the text but maybe you guys have a better suggestion?
thesis.texand some other files that do not exist anymore? I don't know TeXmaker, so I don't know whether it handles projects this way (like TeXnicCenter does). – Werner May 31 '12 at 18:48sudorights, so I do believe it has something to do with directory permissions. But I still can't manage to get things right so that I can launch Texmaker normally. – May 07 '13 at 22:56