How can I update/revert a feature which includes page manager and mini panel components that is stuck as overriden?
Attempting to answer the question:

You should be able to simply re-export the feature to update the pane identifiers in code.

Background info:

There are two parts to this problem.
First of all, features uses a different way of determining whether or not something is overridden, than ctools does. So Ctools consider the state to be "in code", but features, "overridden".

Secondly, the way panes are identified have recently changed. The change initially came about to solve a particular bug, but now causes other problems instead, namely the 'new-X' "overrides".

There are several different patches in the Panels queue that all have different ideas on how this problem should be solved. Currently, I'm afraid to say that I believe you can't do a great deal about this. The current behavior simply isn't optimal.

You can read more in this issue, and the ones that are linked to.