A single .mts file Thru Adobe Media Encoder to mp.4 has No audio - yet other clips are fine.

Try Shutter Encoder, I like it much better than Handbrake.

Use Shutter Encoder to convert the files (before editing) to constant frame rate. Maybe try ProRes LT or even ProRes PROXY format within Shutter Encoder for easy to edit formats with 'better' files size. https://www.shutterencoder.com/en/

Show us what you have on that clip in MediaInfo:

You can use the free MediaInfo program to get info on your clips. Get the program from the link below and using the 'Tree' view post a screenshot of your clip info: https://mediaarea.net/en/MediaInfo/Download

I have a few .mts files, I don't recall what I shot them on, but they are from 2018. I've included some MediaInfo below, I dropped it into a project, dropped the clip onto the New Item button, to create the sequence with the one clip, selected Export (as below) and I got an .mp4 that had audio.