Program segments are edited into individual sequences. The individual sequences are then nested and edited into a new final sequence.
The final audio mix is created by double clicking on the program audio tracks (2) and revealing the un-nested sequence. Audio changes are made to the Segment sequence which, I believe should make the exact changes to the Program timeline.

However, the audio changes are NOT reflected in the Program Timeline.

Steven,

This seems to be a series of statements. What is the question?

Probably better to have posted this in the audio Forum or the editing Forum.

Regardless, welcome.