So, this has now happened to me TWICE before I figured out what was going on, and I wanted to share my findings with everyone so that this doesn't happen to you.
I created a mess of mobile device home screen layout configuration profiles earlier in the summer. I have since upgraded my JSS to 9.101. I needed to scope additional devices to the profiles, so I edited the profile, added the additional device groups, and saved. As soon as I hit "Save," all of the content from the actual "Home Screen Layout" payload VANISHED. Luckily, I had a backup of the profile.
What happened was this: Either in 9.101 or 9.100, not sure which, an option was added to the Home Screen Layout payload screen for "Targeted Operating System," which allows you to select either iOS or tvOS. If you created the profile before this option was added to the screen, nothing will be selected. If you then save the profile while still having nothing selected for that option, the Home Screen Layout payload disappears.
However, if you select an operating system (presumably iOS), it keeps the rest of the payload in tact, and subsequently saving will not delete that payload from the configuration profile.
Do yourself a favor, if you're on 9.101, go through all of your mobile device Home Screen Layout profiles and select your targeted OS now, so that you don't forget and inadvertently delete the payload when you make changes down the road.
Three days later, this happens to us too. When I called JAMF Support, they tell me it's a known issue. When is JAMF going to do an emergency software update to toggle ON the iOS button for everyone? Or are they waiting for all their JAMF clients to eventually botch up their Home Screen Layouts so a call can be placed to Support? It also turns out that Cloud Services can't easily or quickly restore a cloud client's backup and that they recommend you just rebuild your own files. I thought JAMF was better than that.