We have had a recurrent problem with InDesign crashing when trying to update files that have been edited in InCopy. We can work around the problem by finding the few (sometimes one, sometimes several) ICML files that are causing the crash and unlinking. We can then re-export and continue on our merry way. We have tried the requisite deleting of preferences, exporting to IDML, etc., but those things do not help.
Support has not been helpful so far, even saying that they do not recommend using these programs over a network!!! I hope that's a miscommunication issue.
Digging a little deeper, everytime it crashes, it generates a ProtectiveShutdownLog: this log shows 4 APLN that did not load (see below). (This could be correlation, but not causation) Hoping someone from Adobe can jump in and offer some real support.
Adobe InDesign Protective Shutdown Log
06/27/12 08:38:45
Unhandled error condition
Session started up at 8:37 AM on Wednesday, June 27, 2012
Version: 7.5.3 - Build: 333
Error Code 0x20705: "The content is locked and cannot be modified."
Called to process command 0x21a
Command Processor Stack (from top to bottom):
9. Command 0x13513 "Create Hyperlink Text Destination"
8. Command 0x7304 "Import File"
7. Command Sequence "Import File"
6. Command 0x730a "Import File"
5. Command Sequence "Re-import File"
4. Command 0x7314 "Re-import File"
3. Command Sequence "Update"
2. Command 0x8c59 "Update Link"
1. Command 0x8c9f "Update Link"
Registered plugins:
Name ID Version Build Load Status
----------------------------------------------------------------
POSITIONTOOL.APLN 0x19b00 7 5 Load Failed
EDITOR HELPER UI.APLN 0x21101 7 5 Load Failed
INCOPYCOREUI.APLN 0x21201 7 5 Load Failed
INCOPYFILEACTIONSUI.APLN 0x21301 7 5 Load Failed