I've just started a job in a school and one of the first things I was asked, was to deploy a purchased app to the school iPads.
We have a number of licenses for this app all contained in one Excel spreadsheet (obtained from Apple Volume site), some of these license keys were issued through Meraki for staff iPads. However the student iPads are managed through Apple Configurator. I went to the first MacBook Pro which manages only around 20 of the iPads and imported the Excel spreadsheet, where I was expecting to select the keys I wanted to import, instead it added all 80 (including those keys already used in Meraki). I now can't find anyway of removing the already used and unneeded keys from Apple Configurator!
I tried editing the Excel spreadsheet to just include a selection of keys and reimporting it but nothing happens. I also tried removing the app altogether from Apple Configurator (after removing it from the supervised iPads) but whenever I add the app again the 80 licences are brought up automatically.
Did you re-download the spreadsheet again after redeeming the codes with Meraki? That would flag the codes used in the spreadsheet so that when you would import the file into Configurator it would import the codes but not use the already redeemed codes. If you were to add additional staff devices to your Meraki MDM it would also need to be made aware of the codes redeemed by Configurator.
In order to remove the codes completely you would pretty much have to dump the database which means all of the devices you supervised would be deleted and essentially need to be restored back to factory to remove the now invalid Supervision Profile.
The spreadsheet was only downloaded once, we took the last 36 keys for Meraki and pasted them in. I did try removing all the preference.plists for Apple Configurator but that didn't seem to remove the association with the 80 licenses.
The database is in ~/Library/Containers/com.apple.configurator . It will be quite large depending on the number of apps you have imported and other data as well. Mine for instance is nearly 18gb and we have a catalog of about 350ish apps.