Our inDesign file claims that some of the links have been modified even though they have not been. The links window shows 400 of our approximately 1100 links marked with the modified icon, the yellow triangle. When we try to automatically update all modified links, inDesign crashes. This problem started recently, in the last few days or maybe as long as a few weeks. I am using Macs with the current operating system 11.6 Big Sur and inDesign 16.4.
It sounds like you're saying that this is happening with a single InDesign file. If that is the case then the problem may be that there is some corruption in that file. Try exporting the file as an IDML and then opening the IDML in your version of InDesign. You can then save this new file as a normal .indd. This process can remove some forms of corruption in the file. Hopefully, this will be the case here.
Sorry to hear about the trouble you are facing. Could you please share a few more details like:
Is the issue related to a specific document? If yes, could you please package including all the links & fonts and share the document with us? You can upload it to the Creative Cloud (https://helpx.adobe.com/in/creative-cloud/help/share.html) and share the download link here or via DM.
Where are you saving the files & links (Network Drive/ System HDD/ Shared Folder on System/ External HDD)?
Are there any recent changes made to your system? For example, any antivirus, system updates, plugins, or web extensions installed recently.