Do you run Sutcase? They had a recent update that caused this behavior, and have a newer one, I believe, to fix it.
No, using FontExplorer.
Is it resticted to only one or two types of links, or does it seem random? I don't actually have a lot of other ideas, though...
Link type doesn't seem to matter, although it does seem to be the same links every time. I ran permissions repair and cleaned cache files using Onyx, I'll see if that made a difference.
Doubtful. Try disabling your 3rd-party plugins, including FontExplorer.
Are links network or local?
Finally got a chance to test this out. A particular file that seems to give me problems is a template file (indt) that I use weekly to create a PSA for local paper. A couple of weeks ago when it asked to update the file, I did, then resaved it as an .indt file. No problems until today, the update links dialog came back. I quit InDesign, removed FontExplorer from Plug-ins folder, than tried to reopen the .indt file, still wanted to update the 2 links within. Both of these files are stored on the local HD.
Decided to take a look at the linked files themselves and they show a modified date of TODAY and the time is probably right around when I initially opened up the .indt file (about 8 mins ago as of this writing), even though I haven't open these files in months, if not years.
This may be what's happening. Template files always open as new documents, meaning they will have a modified date of "today" (since they're new, they haven't been open previously). Try opening and saving the template as an actual .indd document, importing that document and see if the problem persists. It sounds like a template problem to me.
I don't think INDT is the issue, I open INDT files with links all the time and wrong things dn't happen.
Is it possible that FontExplorer modified the linked documents the first time you tried to open them,
and then, of course, even though you removed FontExplorer, that didn't un-modify them?
That would be my best working theory. Not very satisfying though.
Possibly also overzealous anti-virus software?
[or heck, a virus]