This appears to be an issue only with InDesign and Box Drive.

Steps to reproduce:
1. In InDesign, link to an Illustrator file or PDF with multiple artboards, layers, or pages from the Box Drive folder.
2. Place the file and select a single artboard or page.
3. Save, close, and re-open the file.

Result:
The linked file will no longer update. Perpetually needs updating even though the file hasn't changed.
The workaround is to save the linked file to Adobe Libraries.

Expected:
The file link should show that it is updated in the links panel.
 
System info
    Application: InDesign v16.3.0.5
    OS: macOS v11.2.3, RAM: 16.00 GB, CPUs (logical): 8