Saving the file on to itself and clear its undo history sometimes helps, but in the case of the hyperlinks I mentioned, removing the undo history didn't help. It was the sheer number of hyperlinks that was the problem. It looked as if InDesign allocates a certain amount of memory to hyperlinks, and when that memory fills up there are problems. It does continue to add links, but very slowly. I've no idea reaaly how it works, but memory allocation seems to be involved. It looks as if you have the same problem with links to files.
When you consider the number of links, you should factor out duplicates. I the same file is linked 10 times, the file has 1 link: the other 9 are pointers, they're not really links. @Aprking has 12K unique links, which is not the same as 300 links duplicated 40 times. The latter file still has 300 real links, the remainder are pointers.
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