Using the links pallet to open an Illustrator or Photoshop file, edit it and save it, return to InDesign, InDesign will crash every time. Reopen InDesign the link will show as being modified (yellow triangle with exclamation mark). I can then update the link and continue working.
Mac OS X 10.11.6
2.8 GHz Intel Core i7
16 GB ram
AMD Radeon R9 M379X 2043 MB
No change in behavior after replacing my preferences.
I removed the scripts I had added over the years and it no longer crashed when updating links . . . for one try. Then I replaced my preferences again and it seems to have returned to normal operation.
So, if replacing your preferences doesn't fix the problem, try removing all the extra enhancements you've added and replace your preferences again.