Save your work by exporting to IDML, force the application to quit, then relaunch and open the IDML files.
Attempting to save the file via a scripting interface also fails. Adobe has been unable to reproduce this failure, and hasn't found a root case that can be resolved. Some customers report they have been able to avoid this issue by disabling Preflight. But others report that disabling Preflight did not solve this issue for them. Adobe will continue to try to uncover the root cause for additional solutions.