Thanks for the heads up here. So as someone who had travels on A2/E533 looking into how I should update my .list, I'll put what I'm doing here to see if it makes sense and in case it helps others.
I should remove that segment from A2 and E33 by using lines like
DEU-BY E533 1(A95) MunStr
DEU-BY E533 B23_E DEU/AUT
but I can also keep credit for the part of B23 that goes into Oberau with a line
DEU-BY B23 B2_N B2_S
and the segment north of there to where the bypass will just no longer be TM clinchable.