I think I finally found the solution to this on my end. I hope it works for everyone else.
Get a paper and pen to write down what you delete. I had to undo and redo sends and outputs.
How to fix missing sidechain bus in PreSonus Studio One (hopefully)
Try this first: For the track or channel which is missing a bus in the sidechain menu. (not the missing bus)
1) Set the channel output to the master track
2) Delete all sends going from the channel (if no current sends, add one and remove it)
If that doesn't work, do this to the missing bus:
1) Remove sends that are going to the missing bus
2) Set only one track for the bus input (if no input. make a track, then output it to the missing bus)
3) Set the bus output to your master channel
Can it be prevented?
I think it is a software bug. Why? Because after doing this, the sidechains and busses work normally after putting things back together.
In case I am right, set everything you need to this time in case it goes missing again.
Note for PreSonus QA:
I don't have time to double check, but it is possible that I applied the same sidechain bus to the channel previously. Including, the same VST plugin, except I deleted the plugin and added it again; only this time, the bus was missing from the sidechain menu.