I lost access to Devotion Gardens and Blaze after exiting the game after a game over. That run I was playing solo, with Blaze and Shroom, starting from Devotion Gardens. 

The quests for Zed and Bunker in the Procedural Factory can't be completed due to the bug blocking access to Devotion Gardens.

All other progress was seemingly saved.

Here are the save and diagnostic files.

Endless Dungeon Documents Folder.zip