eitherway when the new AP plugin comes out I would think that the creator could write a small extra script to convert the old db file to the new format for the plugin. Shouldn't be that hard to write an extra script that would read the old db file and output it in the new format.
They both can use the same old DB file so its a matter of just copy your old DB to your new Java protection folder location, thats if the new protection use's the same table names, if new tables are added, that can be done very simple with one simple line of code.