I have a wild and crazy idea; I haven't done this, but as long as we're talking about things that are theoretically possible...
IF you manage to decompile all the code and get a system that you can recompile and run (and I strongly recommend you do that before you make any changes), if you are able to identify where the int is that you want to replace with a long, and then all the direct and indirect references to it, hopefully (because it's just this file size limit that you mention elsewhere) you end up with only a handful of classes.
The decompile should tell you their names. Create new classes with the exact same names, containing (of course) all their decompiled code. Change the methods that you need to change.
Now put those classes in a jar that is searched before the jar containing the application. You're limiting the number of classes for which you're providing new .class files to just those. This makes it easier to see exactly what has been changed, for future programmers, if it doesn't do anything else. It's possible because of the way Java handles its runtime; the step that's equivalent to 'linking' in a traditional compiled non-virtual-machine language happens when the class is loaded, instead of at compile time.