I have work books that link to other workbooks and do not have this problem. just make sure you sync your OneDrive with your computer and open the workbooks on your computer.
I no longer have this problem since I started syncing One Drive to my local hard drive.
I no longer keep files on my laptop but save everything to OneDrive. I update Excel workbooks on OneDrive that have links to other workbooks and I no longer have a problem with changing links since I unchecked "Use office 2016 to sync Office files that I open" on the Office tab in the One Drive Settings.
Solved Maybe- I've have had the same problem for last year with links to external workbooks, however today 03/18/18 I tried the solution of changing setting in One Drive and it seems to keep the links from changing. Right click on One Drive in Task Tray, click on Settings, click on Office Tab, uncheck "Use Office 2016 to sync Office files that I open". I've tested this several times and link remain. I also edited the Excel files using Office online and even though the links were disabled it still did not change them. If anything changes I'll add to this post.
For some reason if you do a Save As each time rather than Save it will not break or change the link. Not a very good solution but it works.
We had to stop using OneDrive because it changes all of the external links. I'm keeping everything on my laptop for editing and then using a third party backup program to sync my files to OneDrive for viewing only on phone and tablet. This link changing is a real Microsoft ***** up.Doug Scott supported this idea ·
The only way I've found to keep this from happening is to do a Save As on the workbook containing the link instead of doing a Save. This way the link will continue to point to the local OneDrive instead of the OneDrive web location. However if you forget and do a Save all of the external links will be toast again.
As a workaround you can do a Save As on the Excel file with links to other workbook and it will not change the links to web location but will leave them pointed to the local OneDrive location.