Audio sync to external audio track

[DannyZB]

My player has the following scenario:

1. A video stream is mapped from an MP4 file using HLS with .ts segments.
2. The audio is converted separately using ffmpeg.

How can I get the audio to be in sync with the video when they are generated separately like this?
I already use -copyts when converting the audio to m3u8/ts segments in ffmpeg.

This need exists because I have multiple video quality levels and a single audio stream, and the video levels are converted separately.

Any ideas what can be done? What is the best way to keep audio in sync?