Yesterday I was creating some project and track templates and at some point my audio inputs (8 analog channels from a Focusrite Scarlett 18i8 gen 2, ASIO mode) could no longer be seen on any audio track input menus. This persisted across several different project files and a reboot or two. Throughout all this, the Audio pages of my Preferences indicated that all 8 channels were available -- they just weren't visible at the Track level.
 
Then for some reason I decided to see if I could just get the 4 mic channels and un-checked the 5-6 and 7-8 pairs on the Input Drivers list. All the sudden I could see those 4 channels in my track input menus. So I re-checked the other 4 channels and now I can see all 8, just like before. 
 
I may or may not have re-started Sonar (or even re-booted) between each of those last few steps, but I thought the sequence might be enough for someone to start debugging with. If it happens again I'll certainly try to pin down what happens *before* the inputs disappear...