Version upgrade

You mean lite version? Yes you can. The licenses and amount paid are timeless. You only have to pay the difference from what you paid before in order to upgrade.

Basically, everything under the folder "UFE\Engine".
If you are not planning on adapting the demo that comes with the project you can disregard the folder "UFE\Demo".

In what sense did it break it?
One thing that can potentially happen is having your editor files lose connection to the dll file they were previously linked to in the PRO version. What you have to do is link them to the open source version of that file.

- Global config files are linked to a script called GlobalInfo.cs (located under Engine\Scripts\Core\Global).
- Character files are linked to a script called CharacterInfo.cs  (located under Engine\Scripts\Core\Character).
- Move files are linked to a script called MoveInfo.cs  (located under Engine\Scripts\Core\Move).

Hum. Yeah that can happen sometimes unfortunately.
There is a way to fix it, but can be a little complicated. Make sure you have a backup of everything so you can restart the process in case it didn't work the first time.
Go outside Unity and using a regular text editor, open one of the data files.

For the original data files linked to the dll, look for a line that resembles something like this:

m_Script: {fileID: 2039538461, guid: 290947d1480294243a72173919bf47d1, type: 3}

There is only going to be one line that starts with "m_Script". That is the one you are looking for.
Now open that exact file type from the Source version and replace the previous line found in that file with the one from the Source version:

m_Script: {fileID: 11500000, guid: 7a72eb99efd94a347a4ab4cc0376dbb1, type: 3}

Each file type (Global, Character or Move) has a different fileID and guid. All you have to do is match that line and save the file. This should correctly link your files without losing the changes you made.

So after connecting up those scripts using Notepad, I ran the game and in BattleGUI strange things happen:  I get a ton of Null Reference Exceptions and When I pause the game in BattleGUI, it looks like the "BattleGUI" prefab and the "Game" object are respawning them selves over an over.  Furthermore, the "Game" object's CameraScript is missing refrences to Player1 and Player2 - Any thoughts on why its respawning itself in the hierarchy?