Database ID does not match and I can't fix it!

On another client computer, not the one I have been using earlier, CheckRequest was up-to-date but SD Matters was not. Both were closed. I opened CheckRequest my usual way (with a procedure), and received a database out-of-date dialog. But now, given what you wrote earlier, I looked at the dialog sheet more carefully and then reviewed the history, and confirmed that it is exactly what you suspected: this is the update-needed dialog for the SD Matters database but it is attached to the Window for CheckRequest. Clicking the Update button results in exactly the failure mode we have been working on.
This would explain the intermittent nature of the earlier observations, why it can fail repeatedly even though I repeatedly installed an up-to-date copy of CheckRequest. I have apparently been misinterpreting the Window that appeared, thinking it was identifying CheckRequest as needing an update.
I now suspect that the change in code that I made did not actually fix the problem, it was just coincidentally installed at the same time that SD Matters was independently updated.
I also think you should be able to duplicate this situation.

I don’t think I have found any instance where the new generation upload to the server malfunctioned. Downloading, yes, but not uploading.

Yes, downloading is where I suspect the problem. I don’t see how it occur with uploading because you would only be able to initiate uploading if the database is visible, there is no way to make a new generation when the database has no visible windows.

Right, because the file that actually needed to be updated was SD Matters! So probably downloading SD Matters would fix the problem.