I'm trying to split audio for a 2 hour blind lets play

[Koopa Rs07]

Why don't you record the streams separately to begin with? Are you recording your mic and in-game audio both with ShadowPlay?

This sounds like an issue with the software you use to split. Have you tried googling this issue?

I like to record big chunks of gameplay and then chop it up in the editor. It's usually easier.

If I understood correctly, you have recorded some videos with audio that you now want to split. To do so, I can only suggest doing that:

1) Download Camtasia Studio 8
2) Run the trial version
3) Follow this guide

Check this out and lemme know if it works.

I'll give this a try, thanks. (Edit: Yeah, it didn't work. The audio shows up with no sound, but the duration is 1 hour and 53 minutes which is correct..)

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