I am at the beginning of an enterprise deployment. Indesign CC2018 on Mac High Sierra.
See Reported Bug notes:
BUG REPORT NOTES,
INDESIGN FILES ARE LOSING THEIR LINKS—
If I open from Indesign idml, the file can update links,
and the option to “find other missing links in this folder?” Is disabled.

Then, if you open an Indesign.indd file, the
File forgets its links,
If you relink, and save the file, it forgets it’s links all over again.
My workaround has been to open from idml,
update links, export again as idml, save the indesign file.
HOWEVER
I still need to open from the idml. So, it kind of makes the indesign file redundant.
The worst part of this is that when updating the links, the option to “find other missing links in this folder?” Is disabled.

I have the same issue

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flat plans Pages and connect with InDesign - we need something like that !!!

Well, thanks, nobody at Extensis told us about this v6.1.7!!!!!! Will try is immediately. Thanks!

Extensis has a new version of client. Version 6.1.7. it should do the trick.

I can confirm that when I rolled back to 6.1.5 the problem was indeed fixed.

Aman, I do confirm that the problem is fixed when returning to previous version of Extensis Universal Type Server Client 6.1.5. Extensis does know that there is a problem, but they don't seem to care about it... Thanks!

I randomly have this problem and i don't even have Universal Type Client :)

Well it seems that the bug is coming from using Extensis Universal Type Client version 6.1.6. The answer from Extensis: Erase the version installed with a Terminal-type command and re-install previous version 6.1.5... I just hope that it will be a temporary solution...

Funny you should say that. I suspected it was UTS this morning while troubleshooting another user within my company. Besides the linking "modified" issue we were experiencing some rainbow pinwheel freezing as well. We disabled UTS and everything worked fine. I even disconnected from the server completely, restarted, and established connection and the freezing stopped, but the modified links came up again. I think there is definitely a correlation. I haven't tried to downgrade my UTS version yet, but will let everyone know if I do and the results. Thanks Uwe.

Hm. I found this in the Forums:

8. Re: Links status perpetually set to "Modified"
MadsDaniel May 30, 2018 11:35 AM (in response to JamieMcKee)
https://forums.adobe.com/message/10413600#10413600

"We are having the same problem on several installations, and this is in our case related to Universal Type Client 6.1.6.
If i disable UTC plugin everything works just fine - I'am contacting there support now.

As a temp. solution it's seems to work if we SAVE AS.
New documents are not having this problem.

:: Mads Daniel"

Hope, that helps.

Regards,
Uwe

Ive been in contact with Adobe Tech support. It is now escalated for a fix and update. The only workaround is to use Indesign 2017 version and not the 2018 version. By using Indesign 2017 you do not get these modified warnings. Ill keep you all posted once I hear anything else.

Same problem here. When opening the file, it is modifying the links to the date and time you open the file. After updating and saving the files revert back to their original time stamp - therefore they are modified again. Very annoying. I have removed the complete CC and installed one by one - still no joy.

I got this too. Closing the InDesign file and reopening it generally takes care of the problem, but it can randomly show up as modified while I'm working on the file, even when the file time stamp is exactly the same as it was before. Also, once the files show up as modified, saving the document makes it so closing and reopening the document makes the modified label permanent until I update all the links. FYI, I'm working off a shared network drive.

Same problem here! InDesign keep asking to update links THAT ARE OK! Overtime I save the file, it keeps putting it back to MODIFIED! ANNOYING!