Exactly this issue arose on GitHub - it is, as you say, because you did
not update the qubes repository definition in timely way.
You can read the issue 

The resolution is to follow the steps in the upgrade script - courtesy
of Marek:
The source of the problem is that in R4.1 we actually stopped shipping own 
duplicated xen packages, and are relying on those from official Debian 
repositories. But the upgrade path requires manual step because of that.
The in-place R4.0 -> R4.1 upgrade tool handle that automatically, but in case 
of manual upgrade, see this part:

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