If you pasted something long, you could possible switch to a terminal (ctrl+alt+f2 or something), and kill the process.
Or you could grab another machine, and ssh into yours to kill the process.
The trick that makes this work, and probably will for you too, and allow you to keep your HTTPS queries, is that Pi Hole will just not ask upstream, if it has the DNS name in the CNAME records. Those CNAME records will have to point to a domain, that Cloudflare doesn't know about. That way there is no other records upstream that will confuse the DNS server and your browser.
The hostname you have in your local DNS records that your CNAME points to, will be something only known locally for you.
Try with nslookup and see if you're resolving the domain to both your local ipv4 address, and the Cloudflare ipv6 at the same time. I am using pihole for my local DNS, and it would give me both my local address, and also the Cloudflare ipv6 address.
Edit
My pihole will ask upstream even if the domain was listed locally. It doesn't ask Upstream for cname.
Awesome!