DiaGraph should be used at your own risk; no one is accountable for any disadvantage caused by using it. However, I swear that I cannot imagine such possibility at all, except that its output file could overwrite an existing LaTeX file. Namely, when DiaGraph acts on the source file example.grp, it always overwrites the file example.tex, if it exists, assuming that it is just the output file generated by the previous run of DiaGraph on (the previous version of) the same source file, which you won't have to keep. Just in case where it is actually an important file, however, its back-up file will be created as example.org; the latter file will always be overwritten without making a further back-up file or issuing an error message---you may fail only once.
Simple solution: Make it a rule not to use the same name for a LaTeX document file and a DiaGraph source file.