I've noticed this issue for a while now but it seems to be getting more frequent. Right now one local channel is missing from my guide on my mobile devices but shows up in the guide on my Fire TV and in the guide on the website. All are set to show "All Channels" and I have swapped it back & forth between HD Only, Favorites, All Channels, etc. to see if it would fix it.
I've confirmed the channel is working- it plays fine from the website guide. I've tried force closing the apps, etc. and it doesn't fix it. I've also seen the opposite happen. Last week I had one channel that would not show up in the guide on the Fire TV, or the website, but did show up on the mobile devices.
I've tried deleting & rebuilding the entire guide database. Sometimes it will fix these issues, but they eventually reappear again.