As long as you have the “Search all open Kee Vaults and KeePass databases” setting enabled, the active database should have minimal (or even zero) effect anyway. It previously also affected which database a new entry got saved into but you can choose from any connected database now.
Kee Vault shows the name of the database, not the file name. Please check that the Isabelle KDBX file has a unique database name.
Also never run more than one KeePass instance at the same time. If you are using multiple local Windows users on your computer, make sure you read about that on this forum and configure custom ports for each user.