You have an AppBuilder Professional license with 2 seats that is part of your account. With the new changes introduced with the new Telerik Platform product, in order for the users that are added to these seats to be part of this license, you should login and invite them as members. More information on this procedure is available in the following articles:
This workflow might not be the most intuitive one and it is in our plans to improve this functionality.
On a side note, you not being one of the licensed seats is not true, you would always take one seat and be the administrator for the purchased license. So basically what happened is that both of your devs have started an AppBuilder Starter license with us (which is 30 day trial), until you add them as members. As you have two seats only, you would have to give this account to one of your devs in order for them to be able to collaborate and use AppBuilder, otherwise you would have to purchase another seat.
About the missing code - no migration has been done yesterday, all migration took place during the weekend. With that in mind, have your developers restarted the AppBuilder IDEs since? The old IDE Graphite would not be able to work with the new platform and needs to be updated to AppBuilder.
In general it is best practice to always commit and push project changes to a git repository of your own, so you have a backup of your work (as our license does not cover backup of deleted code, rollback and revert actions).
Do let us know if further help is needed.