Question

While actively publishing a Document Definition and just browsing to a subfolder of the project directory you receive "sharing violation" type errors and completely corrupt the project.  The corrupted project is no longer able to locate the Document Definitions.

Answer

FlexiCapture locks the entire project directory whenever it is updating the project and Document Definitions.  The only way to recover from the project once it is corrupted in such a manner is to either restore the project from a backup or completely recreate the project from scratch.