Okay. I checked my tablets file folders and the books all appeared to still be there, Calibre Companion just wasn't seeing them. I verified against my other tablet that the folder names were the same. (I think one of the issues with new Calibre Comapnion is that it moved and copied all the books to a new folder. I am so thankful I didn't actually open "new" Calibre Companion and so they remained where they should be.)
I changed the folder from default to the actual folder name in the where to store books option. Then I changed it back to default folder. After that I was able to get Calibre Companion connect to Calibre, and it "found" most of the books. This took over 20 minutes. It was odd which ones I know were on there, but it didn't find 70+ of them in my main library and many more in my vault library. I had to disconnect and change libraries (which is usual, and I am always careful to do so before switching libraries).
Finally figured out if the title was showing but no cover I needed to resend as it didn't recognize it as on device even though it showed up on the list on the device. Really odd as some showed in Calibre on device and other didn't so no other way to tell. That took over an hour.
But all seems well now. I am able to send books to Bookari and read them.
Really happy as I didn't want to resend all 3000+ books I have on there between 3 of my 4 Calibre libraries. This was a mess, but I was able to fix it in less time than that would have taken.
Highly recommend not accidentally updating CC though
I really wish there was a way to simply block apps from looking for updates on Android.