Never mind, it looks like the following happened:
1. I created a new atlas using the atlas creator.
2. Added some sprites to it (another atlas broke).
3. Created some controls in scene (new atlas worked as normal).
4. An existing atlas texture had been renamed to " ".
5. The associated material was no longer associated with texture (from 4.).
6. Prefab was no longer associated with material (from 5.).
Before creating the new atlas, the atlas which broke was previously selected inside the atlas creator interface.
This is a bug, but I have managed to correct the breakage
