Hmm... since Windows accepts paths with / instead of \ separators, maybe it'd be a good idea to save the paths in / separated form in the project files and convert to \ on on output/load?
We tried that... this breaks UNC paths and does not work on Windows98/ME.
Not even if you use wxFileName(path) (possibly with an explicit wxPATH_UNIX second argument if necessary) to convert it when you're loading the project file? Or just a dumb wxString(path).Replace("/", "\\") (#ifdef __WXMSW__ only, of course)?
...
I suppose you could always XML-ify it a bit more:
<Path><PathPart>src</PathPart><PathPart>file.cpp</PathPart></Path>
(j/k :P)