I recall that once upon a time when your file was missing links, if you relinked one file, Illustrator would find all the other linked files in that folder and ask you if you wanted to relink them. Now, Illustrator can only seem to find just the file you are seeking to relink. If I have a file linked twice in a document, Illustrator only relinks one of them, even through they are identical. What happened to this very important time-saving feature? I've been using this application professionally since Illustrator 88, and while it's come a very long way since then, in the last few years it appears to be regressing instead of progressing with the above mentioned example as proof.
Thanks for reaching out. Would you mind sharing the version of OS and Illustrator? Also, I'd recommend checking out Update Links option under Preference > File handling & Clipboard and make sure it is set properly as per your requirement.
I am also attaching a screenshot for your reference:
(I had a long time ago uncheck the new the includ linked files)
I checked above preterences, they are the same as yours suggested, so not solution for me..
I have windows 10, and it is uneven issue. I have files on computer. I am used to organizing work around this link problem and I probably challenge the illustrator with amount of linked files and pages..