I was up until recently using cocos2d-android to work on my project until I discovered this glorious website.

I would prefer not to lose a few weeks worth of work. Is there any way that I can "call up" to the Java code and present it to the user or will I be forced to recode everything?

You can read documents on android.com for how to invoke java codes via JNI.
But my suggestion is to translate the java sources into c++. It's very complex to mix your 2 opengles drawing views, one in cocos2d-android, another in cocos2d-x.