Personally I install the new version into the same route folder as the previous version and then once I've finished I delete the old version. Some games have to be set up in the main C:\ directory but most games you can crate another folder in your games folder and that will be finesafely if you have have copied .24 saves to .25 or those are in appdata or linux/max/android equivalent.
if there is persistent.save somewhere where game knows to look for then settings will stay.