Audio out of sync after using media encoder

I have a 12 minute video i want to edit, my first problem was that the entire video was out of sync with the audio. The audio was approximately 1 second behind. I followed the instructions of using adobe media encoder and I put the video back into premiere. Then the audio was fine until the last 2 minutes.  the audio was 1 second ahead of the video. How do i fix this? I only wanted to do 2 very simple edits to a simple video and ive spent hours trying to figure this out. 
PC specs 

CPU intel i9

GPU RTX 2070 

RAM 16 gbs of ddr4