I also noticed one or two icons disappearing with the "Windows 11 style" setting on Explorer Patcher. I have switched back to "Windows 10 style" with "always combine icons," which looks almost the same.
I can't seem to get notification tray icons of selected apps to persist on the taskbar but that's a trade-off I think I'm willing to make if the other icons stop disappearing. See updates to my post on this above, with screenshot.