Save Player Data on Update

I want try out my mod with some of my friends on a server, but also to update the mod regularily (you know, the kind of 1.1 and 1.2 Update, you will understand) but I would have to replace the JAR file every time, which would delete all of their player data, like player persistent variables, how do I keep their progress?

For example, if there is a quest system, and they got to a specific quest, or if they have a number variable that is at a certain value, if I switch the JAR file, all of that progress would be wiped. How do I go around this? Thanks in advance!