the unmanaged layer sits on top of the managed layer, so if there are unmanaged customizations, you won't see the managed changes. What you describe is pretty common--if you go and make a change to your flow in production, it creates changes in the unmanaged layer.
And that is why @Anonymous that connection references are a good thing--they now allow you to import solutions and will prompt you to set your connections when you import the solution, eliminating the need to make changes to the flow in production and also eliminating the issue with the unmanaged layer. One of our recent podcasts was about it. https://crm.audio/connection-references/
Note if your flow was already created and does not have connection references, you need to reimport it for the connection references to be created. Also, if you are using package deployer to deploy your solution, there is currently a bug where the flows with connection references are not turned on automatically.
So all in all a very good thing. Not perfect yet, but a step in the right direction.
