Unable to reproduce the issue on x86/64 r12230-5715b21f80 - at least a simple test with iptables -t raw -I PREROUTING ! -s 10.11.12.7/32 -i br-lan -j DROP works as expected here. My desktop still can access the net, traffic from all other devices times out.
Well there was a bug in LuCI with displaying certain iptables rules with exclamation marks in them, due to a bad regular expression. Related issue was https://github.com/openwrt/luci/issues/3642.
You stated "no longer appear in my running config" which sounded to me as if
a) the rule itself is not working
b) not appearing in iptables-save
So I suppose this has been a LuCI display issue all along.