Stories missing from IC Assignments panel after links are updated in ID

OS: Mac
ID version: 20.5
IC version: 20.5

Hello, all. For the past three months we've been running the simplified workflow where the designer exports ICMLs to a shared cloud server (we're using Egnyte) and IC users open the INDD to work on.

Today for the first time, on a particularly complex file, we're running into what I see from searching the forum has been a bug in at least one previous version of ID — the first time the designer opens the INDD after a series of edits in IC and is prompted to update links, the links to all files updated in that process are missing from the Assignments panel the next time someone opens the file in IC.

Thus far, at least, the stories do remain editable even if they can't be seen in the panel — editors can still right-click in the story in the layout and check it out/in, and their changes are subsequently able to be incorporated the next time the designer opens the INDD and updates links.

I've also confirmed that if I right-click on Unassigned InCopy Content in the Assignments panel and Check Out All, even the stories missing from the panel are checked out, so this doesn't seem like a showstopper, but it will be alarming when editors start noticing.

Are others noticing this behavior in ID/IC 2025, and if so, have you found a fix?

One other thought — the mother version of this file was created in 2017 or 2018, which would have been around the time of version 13 where this bug was seen before. Due to the aforementioned complexity, every year the previous year's version of the file is duped and rebuilt-upon, so the flawed DNA of the original file is possibly still in there to some degree.