@jackryan ....... You can use mkvmerge for this synching audio with the video as well.
See the Format Specific Options tab .... you can delay/advance the audio file to synch with your video.
Some tips:
1.) Prior to the actual mkvmerge, you can check the time needed (this is quite tricky since audio synching is usually in msec and we all want it to fit just right with the video) using VLC or KMP >> See track synchronization option.
2.) Once you get the time delay/advance needed (example: +2msec), you can now use mkvmerge for synching during remuxing.
<Optional>
3.) Since we dont want to remux a whole movie only to find out in the end that it's still not synched (or needs a bit more finetuning), I suggest you use the SPLIT option of mkvmerge so you only remux a small portion of the movie .... this would be enough for you to check if it's synched just right. Say remux only the first 3 minutes of the movie. Based on my experience, its more efficient this way.