Indesign refreshes all references after one change in document - a lot of waiting in local network

For anyone still experiencing this in 2025...

The only thing I found to help with this issue is to manually open all referenced documents. You can't disable the check, but you can skip the open and close in the background part, which takes the most time. 

If I work with indb I often work without opening the indb file to speed up things. At the end I open it of course to get everything updated in a single task. 

If you turn off preflight, would it help you?

I don't typically work over a network - but recently my desktop & my laptop both failed within a few days of each other, so I've been stuck for some weeks working on my backup computer with an HDD, an actual stack of magnetic spinny-disks, so my computer sometimes performs as if I am working on a slow, glitchy network. I found, like you, that InDesign files that had cross-references to other files work very slowly. My strategy was to simply open up all of the necessary files in the background, so that I wouldn't have to wait around for it to update all of those cross-references.  You could probably do better by copying your files locally, assuming that you have a recent machine with sufficient RAM and a sufficiently fast SSD. 

I don't know of any way to supress InDesign's background cross-reference checks. I've always thought it odd that using live cross-references would bring InDesign to a halt, when there are clearly controls to update xrefs manually in the flyout menu on the Cross-References panel. Many years ago, when I was stuck working on a slow, glitchy network, what I did with such files was to write my own Javascript that would update all of my manually created cross-references. Other than "not using InDesign's native xrefs and rolling one's own," I'm not sure what else I can suggest for you.