The dependencies of the make?? shell scripts and the tbto?? transformation programs are somewhat subtle. In general, if you've changed your XML file significantly (e.g., you've added a new graphics), you have to call tbtolatex in any case, because only then all make files are up to date.
Then you should call makeepss, makepdfs, and makewebs with the name of the graphics as argument.
Then you can do the transformation to HTML or DocBook, or call (pdf)LaTeX.
If you want to update your index or bibliography, call the transformation to the desired format, call makeidx or makebib respectively, and then the transformation again.
You can't destroy anything: In the worst case one call is waste of time.