I have a PNG sequence I rendered from animation software. It is 24 fps.
I import into Premier Pro. I change the frame rate from 29.97 fps (the default when imported) to 24 fps (right click, Modify, Interpret Footage, set "fps" field to 24).
I drag the clip into a new sequence with the audio track. The lips and audio align during playback (but its sluggish working with image sequences).
I do a render and replace of the PNG sequence (its faster afterwards). The clip ends up the same length, but the lips and audio no longer align towards the end! And the end of the video clip is chopped off.
I attached a recording with the original PNG sequence and the render and replace result, and the audio file. You can see the mouth opens lined up with the audio (I am just saying "baaa baaa baaa") at the start for both, but the render and replace is wrong at the end.
My guess is render and replace for a PNG imported sequence is not fully obeying the updated frame rate. The clip is the right length, but its not using the right frame rate to render it to a video file.