This used to be mildly annoying but now its a pain.
Randomly indesign will decide that a link to another indesign file is miffing a link within it. You open it up and there are no errors. Sometimes if you make a slight change to that file and resave then it updates fine, but more often than not now it simply will not have it, complaining there is missing links when there is not.
Is there anything to be done about this?
This might be a server issue. I suppose you work on Windows with a remote server. This is happening often. That's why I recommend not to link INDDs directly, but export a PDF/X-4 (without any image compression and resampling) and link that instead.