After merging my audio and my video, only a portion of my audio is merged and it gets cut off. I have already checked that the audio file is longer than that but right now, only 43:08 of the audio clip (which includes 2 lavaliers and a boom) is merged with the video. The video is also longer than 43:08, which means when I try to insert the merged file into my timeline, the audio suddenly gets cut off.
The audio sampling rate is most likely incorrect in respect to the rate in your timeline sequence. This is the most common source of such problems. Check audio rates in the squence, timeline, and footage, make sure they all match.