Hi @ray,
Thanks for your question!
This is happening because this agent you are trying to merge is linked to a record in the SpExportSchemaItem table (a system table used in Specify 6 to map Specify fields to schema concepts via the Schema Mapper).
Specify 7 is not currently aware of this table, resulting in the pop-up error you see when trying to merge those agents. Despite the warning, have you been able to merge the agents successfully?
The warning you are seeing is a known issue we are tracking on GitHub (#4814), and we have a fix we are readying for a future release.