FFmpeg concat video and audio out of sync

This two step process should work

Step 1 Pad out the audio in each segment

ffmpeg -i segment1.mov -af apad -c:v copy <audio encoding params> -shortest -avoid_negative_ts make_zero -fflags +genpts padded1.mov

Or

Generate segments with synced streams

ffmpeg -y -ss 00:00:02.750 -i input.MOV -c copy -t 00:00:05.880 -avoid_negative_ts make_zero -fflags +genpts segment.MOV

Step 2 Concat

ffmpeg -f concat -i segments.txt -c copy test.mov

where segments.txt consists of the names of the padded files.