It’s not officially supported, but you could try specifying a database path relative to the default app directory.
In config.json, add
"databaseFilename": "..\..\EncryptedDir\db",
Replace the path with the correct one for your scenario. I’m not sure how relative paths are specified on Windows, but it should be possible.
Once you change the setting, start Everdo and it will create an empty database in the specified localtion. Once you verify that the database is created in the right place, you can replace it with your actual database from the original app directly.