Yeah, basically I've lost all sound on my rear speakers with v2.0. I have no idea how to fix it.

Hang on, let's be clear about this.

It's one thing to say "when I set the fader to the rear nothing makes any sound", and it's a completely different thing to say "my rear speakers make no sound no matter what".

We've already established that the former was supposed to be happening all the time and that the software upgrade couldn't have changed that.

If the latter, then, based on everything you've already told us (that only the front outputs from the player were connected to the two-channel-only Bose amp), then the software upgrade also has nothing to do with it. If the bose amp drives four speakers from two inputs, and the front speakers are making noise, then the rear speakers must also be making noise.

Unless, of course, the Bose amp or the speakers are fried. Again, unrelated to the upgrade.

One thing I can see as being possible: Your rear speakers are working, they're just mainly bass speakers and you've EQ'd the thing so that it's not putting out much bass. Just turn up the bass and all should be well.