Here is a relevant link to the same issue:
Steps that I took in my project to produce this problem:
When I re-opened the project, I got the error message about the project using alternate outputs even though there have been no recent firmware changes or changes of SD card, etc.
As far as i could tell it made 0 difference, just clicked ok and everything was fine every time I’ve seen it… I think anyway. There’s a fair few random bugs though so it’s hard to tell what’s causing what sometimes.
Have you noticed it making any kind of difference after pressing ok?
This is fixed in the next release.
Thanks Mickey!! 
@kiddles Yeah, two of my tracks cut out. The sequence data for both of the tracks were still present but the tracks were not audible-- mix and level would not change this, neither were null. I think it was when I reassigned the outputs to both of the affected tracks, they worked fine.
Not sure if this was an interrelated issue or not, but eventually, the mixer faders became locked for the same tracks at a later time, where the only solution was to clear the sound from the two affected tracks and to reassign the same samples from the project folder so the mix faders were responsive again.
You may have more than one issue happening together. This alt output problem does affect choke groups though, so you might have 2 tracks that are basically choking each other or something. I reported this in May of last year and it was recently marked fixed. That said, I wish they would release an update with these bug fixes in it. I could care less about the live looping and feature upgrades. I just want the machine to do what it should without the hassle of the current bugs…
@merk I appreciate the time that you took to reply to my post. I actually had my choke groups in check, so it wasn’t an issue with that-- but thanks for pointing that out. I hear you, I know that they are working hard on getting us the release, I have faith in that & what they are doing-- I’m glad they marked your post as fixed though, shows that the bugs are being looked over and tested
Might have caused something I figured was unrelated and didn’t notice immediately then, not sure. Either way looks like it’s fixed thankfully
Aaaarrgghh. This just happened to me for the first time, however, I’m unable to recover. I switched the outputs from the two tracks that are inaudible - no joy. The events are all still there, pads still blink when they’re supposed to play, volume and gain has no positive affect.
Glad this is fixed. Now come on update…
@elsaddiq Clear the pad and reassign the original file if you can as a temporary fix, all events are there like you said 