So, to make the long story short, here's a warm tip for everyone: don't use several VPP accounts with the same apps purchase for managed distrubition at your business/school. What has happened with us was this:

1. we have two VPP accounts


2. some of the apps (let's say iHomework) were purchased on the VPP account 1 and VPP account 2


3. when we switched from redemption codes to managed distribution, only the purchases for individual accounts were converted, of course, because they belonged to that account


4. when we scoped an app (i.e. iHomework) to a user from the VPP 1, and then the same app to the same user from the VPP 2, JSS did not check whether that user already had the app assigned to them, and assigned the same app to the same user twice, each from different VPP accounts


5. this has now a huge impact on our daily operations, since the users don't have apps available to them, and we are working with Apple to have all of our purchases from VPP 1 transferred to VPP 2, so this doesn't happen again