There are a few variables that surround this situation (i.e. how your VPP accounts are set up with locations). That said, we ran into a similar situation recently. We have multiple VPP accounts for multiple locations, with problems occasionally compounded by having multiple admins working to deploy apps to various locations. Over time we have had to go so far as to recreate a VPP setting in Jamf Pro (once only). At our last token renewal, the wrong VPP token was uploaded to one of the VPP locations. Within minutes, I was able to generate and upload the correct token for that location. Content was immediately populated in our Volume Purchasing page in Jamf Pro.
Addressing your specific problem, you should be able to generate the token for the correct location (the other one), upload it into Jamf, and see your content re-populated. Let us know how it works.
