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Something is wrong in your file.
It sounds like the FPGA itself if selecting that causes the crash.
The usual fix is to archive it out then in but if you cannot do that then it needs to be sent to Zuken for repair.
But that is only for maintenance customers.
So your stuffed if not on maintenence.
The only option I can see is to copy everything else that does NOT cause it to crash to a new file, save it at each section you paste in.
Use the selection tools to select board outline, every thing etc apart from the area that causes the crash then copy them.
Paste into a new design, save and ECO update it.
Then you only have the bits that caused the crash to redo.