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At first look it is a network access problem
(i.e. INDD opened from network disc, assigment from network disc, same graphic links)
It could be hard to check but if you run it completely local - do an error occur?
At least if only INDD can be moved and opened on local machine - it can help.
I'll give it a try.
One more thing to mention. Once when this happened, the links palette was empty beside many images on page and incopy stories ?!?!
Can you recall any kind of script that could be run from InDesign at the time when this happen again? Maybe anything that could alert some error or message?
In case of link palette it can be "refresh" problem only.
Depending on network access breaks - my ID get frozen pretty often and no matter if any script is runing or not. It depends on how big file is proccessed rather. In this case no code can be executed anyway.
However on my side I can see a system alert, something alike "the network file is unaccessable or is changed in other proccess."