This is not so much an answer or suggestion but a relative experience reply...
In the past, and currently, when using DB connections in a python script I have created a connection in a folder outside of the AppData directory, i.e. C:\Scripts\DBConn\my.connection.sde
Then I reference the DB connection file in that directory for my models and scripts.
This has always been beneficial, especially if I want to run the scripts in a batch environment.
Finding "Database Connections" has been an issue many times prior to using the above example. It has definitely saved me a headache or two.
All the best,
Chris B.