We have had similar issues but with linked solo files.
All of our masters are linked to a border file, starting from our template file this is a generic border but we have one for each of our repeat clients with their address logo, etc, the idea being you select the all masters in drawing manager, link to the proper client border file and they are all updated at once.
All of the client files have been resaved as AC13. And in the template all the paths have been relinked etc to the AC13 files. But when you select the files to make the change, it doesn't stick. You can select the files, update the files and they get the green checkmark but as soon as you exit the DM and reopen it they are all listed as missing again.
Happens regardless of which client border is linked to, whether its absolute or relative path, etc.
kevin s burns, AIA
massachusetts, usa
AC25 (1413), since AC6
Windows 10
Intel Core i7 -8700 @ 3.2 GHz~ 16 GB ram