One thing that REALLY bugs me about MODs is the fact that every one I have used has a little "A new version is available..." sign on them. Would it be possible to add a (global) boolean (the true/false one) variable at the top of the source code. When set to true (which in the public source code it should be by default) things like updates are turned off.
Turn of your internet or make a proxy that blocks TPT. It will not say that an update is available. But this method makes you not to see any saves.
Another is to always get the latest version of their mod, but is not always guaranteed.
The sure solution is to get their source, edit defines.h 's SAVE_VERSION and MINOR_VERSION to 44 and 7 respectively (This is the current version) then compile.
My version doesn't show that cos the version is above 44.7, but now I can't make it any higher, it's version 45.8, I've put in version 60.5, because v45.8 was ages ago and it stays at 45.8.