My Name is Ben Lounsbury and I am having this issue as well, and have been encountering it at random for about 2-3 years now. My main cause that I have seemed to widdle down to over the years is: un-packing take folders (Let's say audio 1-5 [5 takes]), then removing one or two of the takes (lets say audio 2 & audio 4), then continuing on as usual using the 3 remaining takes as some form of a unison sound etc. Then, as I create new inst tracks, and new bus sends, then ultimately new AUDIO tracks, the creation of new audio tracks (in affected/bugged sessions) starts to push everything out of order when it reaches the CURRENT audio track that's next to use. So, sometimes the issue has already taken place long before you actually realize and are able to see/notice its' effects. So in this scenario when I initially recorded 5 audio takes into a take folder, then unpacked them & deleted audio 2 and audio 4 cause they were not the hottest takes, normally the next audio channel created would be audio 6 (after the 5 takes), but somewhere when Logic updated to their dynamic channel assignments (ever moving reserved audio 3 for preview channel, and inst 2 for click channel) to save space as it takes over any unused audio before it continues on with 'audio 6', the bug was born. So when you create another audio track it would be audio 2 first (the one you already deleted) and the next would create audio 4 (also already deleted) and your problem wouldn't surface just yet. Then, when you finally create your next track, that third track will be audio 6... at that point it shifts EVERYTHING out (Busses, Aux sends, Inst channels [including the dynamic re-assigning Click channel]), and you lose the ability to hear click, and all of your bus sends are now sending to the wrong effect strips and everything is out of whack and cannot be un-done except by creating a new un-bugged session and moving everything you can from your corrupted session to the new one, and the bug in the dynamic track assigning will be no more.... of course, until it randomly happens again :/.
The environment window holds the details of the bug somewhere as the preview channel (for apple loop referencing in a project) is defaulted to a reserved audio 3 channel, until you start creating audio channels, then it should dynamically move three audio track numbers ahead of your current audio tracks created. The click channel, which defaults at inst 2 and dynamically moves appropriately to its one-slot-ahead reserved inst channel whenever you create new inst channels (e.g. if you have 3 active inst channels the click will be on reserved inst 4. if you have 5 active inst channels, the click will be on reserved inst 6, and so on...).
The biggest issue with this is that it is Intermittent, and not caused by some mis-command, or improper use unfortunately. Trying to re-create the issue, I am probably successful once out of every 5-10 times, doing the same thing to cause it every time (unpacking take folders, then removing an audio channel, then creating [or importing] another audio channel, then working the audio track numbers up until the tipping point and throwing everything out).
I currently have a case open with apple support regarding this, and their technicians and coders are even having difficulty identifying the origin of the bug. So I am in the process of remotely recording some sessions with them that include the issue so they can analyze it and hopefully find a solution for a future update.