Following your advice, I temporarily removed some of the chapters from the table of contents.
My supervisors asked me to rename one of the chapters. Even though the project wasn't compiling, I decided to rename the chaper anyway because it would be helpful to have it named properly once the system was cooperating again.
The error stopped, and Flare created the .pdf. I'm not sure if this is correlation or causation, but it's great to be back to work.
