We just pushed a fix a few hours ago which resolves the issue with the empty content manager and mods disabling. The update will be applied the next time you start the game and mods will stay enabled.
If you have the 0/0 mods issue, then please restart the game so it can generate a fresh userGameState file and you can start enabling your mods.
If you have the 0/0 mods issue, then please restart the game so it can generate a fresh userGameState file and you can start enabling your mods.