I use animations or timers. I'm already using them to handle timing for the audio player. I use the same animation that fades the screen out to fade out bgm audio, the same anim that spins my bullets plays the impact sfx on the last frame, etc. If there's no relevant animation, I use a timer.
It seems like you might be using the same audio file, just cutting it short for one use case, which would be a perfect time to just make a shortened copy of the audio file. I use VLC, and can say it's more a media player than a media editor. I didn't even know it had such functionality. Audacity would likely not cause the issue you got from VLC.
If it is in fact multiple different audio files all needing to be cut to a specific duration depending on circumstances that vary in-game, then I believe you will want to either use Timers or Animations.
I'm no expert, there may yet be a better solution or at least a more efficient one.