I did the following on Fedora 44. Make sure you have developer options and debug via USB authorized.
- Dumped my log, which also gave me a record before changing anything:
adb shell content query --uri content://call_log/calls --projection _id:date:type:new:is_read > calllog-before.txt
- Checked what was flagged unread:
grep -o 'type=[0-9]*, new=[0-9]*' calllog-before.txt | sort | uniq -c
Type codes: 1 incoming, 2 outgoing, 3 missed, 4 voicemail, 5 rejected, 6 blocked. On my phone every missed call was already new=0, while hundreds of incoming and outgoing calls sat at new=1.
- Cleared the unread flag on everything:
adb shell 'content update --uri content://call_log/calls --bind new:i:0 --bind is_read:i:1 --where "new=1"'
- Verified:
adb shell content query --uri content://call_log/calls --projection _id:type:new:is_read | grep -o 'new=[0-9]*' | sort | uniq -c
Badge cleared immediately, no reboot required, and no call history was deleted.
PS: This only clears the flags. It does not fix the underlying issue (if there is one). Bottom line: I expect the count to come back..
Very late edit: the count never came back. It stayed clear. Once again, I was wrong 
but happily so.