Audio goes a frame or two out of sync after export premier pro
This may be due to framerate problems.There are two types of 24 fps.
"True" 24 fps and 23.98 FPS.
This mostly doesn't make any issues, but stretched over a longer time, this can change the video duration. For a 45min video, this makes 64800 frames, instead of 64746.
This gives a difference if about 2.25 seconds.

After trying to delete the pre-rendered files as you said before, try to change the sequenze settings.
Before you do this, MAKE A COPY!

If this doesn't help, another way would be to try another codec and or container. So try h.265 or HDx or avi... It may be that those codecs don't have these problem