What
should happen is that the version that is set in the Workspace Marketplace SDK -> App Configuration -> Add on script version should reference the saved version of the Apps Script project. Every Apps Script project version
should have it's own appsscript.json file. So, any editing that you did of the appsscript.json manifest file should not have any affect at all on the add-on. That's what
should happen. What
actually happens on Google servers to match file data between different locations we may never know. If the add-on
is referencing the current development version of your appsscript.json file, then that's a bug at Google. But I don't know how you'd prove that. You probably don't want to intentionally make your add-on stop working in order to prove to Google that there's a bug they need to fix. Strange things have been happening. People are reporting that the bound Apps Script projects have suddenly disappeared, but for some reason the code is still running. I had one of my add-on users report that all their settings are now gone, but the add-on is running correctly. I had another add-on user report that they needed to reauthorize the add-on after I published a new version.
So, there's something really messed up at Google with their data.
If someone else reports the same problem, you could create a new issue on the Issue Tracker and post back here so that anyone who is affected can "star" the issue.