I think what you describe is one of the problems upcoming with the increasing complexity of Plone's stack, and one of the reasons, why it is not recommended to execute a re-install anymore, but to provide a profile for each version of the Add-On, via upgrade-steps (as Mathias mentioned). That increases dev-time significantly and results in even more conflicts, of my experience. Here are the refering docs:
http://docs.plone.org/develop/addons/components/genericsetup.html#add-upgrade-step
Elizabeth Leddy once wrote an Add-On to ease that pain and I can confirm it does:
https://github.com/ampsport/amp.ezupgrade
And the great guys from FTW, too, I never used it, but looks promising:
https://pypi.python.org/pypi/ftw.upgrade
Neither used this one, even claims to have some extra goodies, like cleanup broken OFS objects and R. Patterson's on it:
https://github.com/collective/collective.upgrade
As we're here, the first good doc I could find about it ~ 1.5 years ago, comes from Uwosh, of course:
http://www.uwosh.edu/ploneprojects/docs/how-tos/how-to-use-generic-setup-upgrade-steps
Another solution can be, to check, if it's an initial- or re-install, and set the properties programatically via a Python-script, conveniently called 'setuphandlers.py', like described in this answer:
How to check, if my product is already installed, when installing it?
That way one can still trigger re-installs without blowing it all up.
Lastly, a lot of the GS-xml-files understand the purge
-property, setting it to False
, will not overwrite the whole file, just your given props. This might, or not, apply to your case, you can find samples in the above referenced official doc.