Tried several times, including again this AM. No luck. Have a case open with Meraki through the dashboard but the last communique basically said to try what you suggested and to call in if that failed. Unfortunately, we're under the free-100 not an Enterprise license, so no calling in. Will have to poke support again via email or dashboard and get them to keep investigating. It's very strange since we have 460 apps under MDM -> VPP -> Licensed Applications and 46 under MDM -> Apps, so it's exactly 10% of the apps that are showing up.
I've tried going to MDM -> Apps and importing licensed iOS apps from the menu. If I select all apps and import, it *appears* to be successful - but when you look at the new apps in the list, they will show "Invalid Date" under "Last Modified" (and of course have lost all of their scope information) and if you click the "Save" button, nothing happens - it still shows unsaved changes. If you reload the page, it warns that you may lose unsaved changes and, if you sitll click "Reload", you do in fact lose changes and it goes back to only showing 46 apps.
If I try importing licensed iOS apps and only select 1 app that is currently not listed under MDM -> Apps, I can import it and save changes. The app will then have scope set to "disabled" and show the correct number of licenses available but no devices within the scope. If I set the scope to what it SHOULD be and save changes, it then shows the correct number of licenses available and also shows the current installation information - including devices which it was installed on before Meraki lost its marbles.
It is going to take days if I have to go through and re-import each app one by one and set the scope. I shouldn't need to do this. As far as I can tell after combing through the limited logs visible in the dashboard, nothing was done via the dashboard that should have caused this which means that it's a bug of some sort in Meraki. I want Meraki support to fix this.