Hi Daniel,
Did you upgrade your Server site to 10.4.1 BEFORE upgrading the ArcGIS Data Store to 10.4.1?
I am guessing that you have Portal for ArcGIS deployed with a hosting server configuration, which means a Server site is federated with Portal. When upgrading a federated Server site with Portal, the order in which you upgrade (Portal vs. Server site) does not matter. But for the hosting server (e.g., Server site with ArcGIS Data Store), the order does matter and you need to upgrade the Server site first, then upgrade the ArcGIS Data Store.
Hope this helps,