Video or Audio always out of sync

I’ve been frustrated lately on a project that spiraled into something that shouldn’t be this difficult.

I downloaded a mkv file and decided to extract its files using mkvextract.exe. I wanted to edit it and include something in the audio track (With permission from the original creator).

I edited one with audio but didn’t increase or decrease the audio length. It’s the same, just with an added soundbite. Using Audacity, I exported it as an ACC (MFA) file, but when I multiplexed it all together: the video was strangely out of sync, at first for a few seconds, until minutes, and when I clicked at the end–the audio from the climax was playing during the credits.

I had no idea what was going on. I thought it was the audio format, so I changed it and exported it again as a WAV file. Multiplexed, but the problem remained the same.

Video: HEVC file
Audio: PCM (WAV OR M4A) and AAC
Includes chapters and subtitles.
Using Windows 10

I would also like to add I’m completely new to this. I thought adding a simple small soundbite would have been straightforward and quick. But it turned out far more difficult that it became baffling. I downloaded all these tools today and would love a solution or help.