A good approach would be maybe to create a develop top level VI which contains all the top level VIs of your entire project. Open it up, press shift and the run arrow to masscompile everything in memory and then do a File->Save All. (Create a backup of the entire directory first, for instance by packing everything into a ZIP file, for your safety)
Chances are that now the internal paths are all fixed up and should work. Rolf K
