Hey,
Thanks for checking in!
I forgot about this for a while because we have a bit of a workaround - but we still have the wrong connection assigned to a Connection Reference in a Production Managed Solution.
Because the connection reference is used by both Flows and PowerApps, I would like to change it here:

Obviously in an unmanaged solution I can Edit this connection reference. However, as a Managed solution we were able to assign the Connection to the Connection Reference during our first import, but do not know any mechanisms to change this ongoing.
FWIW I believe this should an available feature, especially as organisation may mature to towards more modern authentication types, segregation of duties etc - in which cases the need for new Connections may be required (not just editing existing ones linked to Connection References).
Thanks for helping!