We don’t know where the issue lies or how to fix it, either. Generally the best way to find out is to reproduce the issue and investigate it in place.
That means if you want help, you must help yourself in some way. Either by hiring a professional to investigate privately, or sharing something we can use to reproduce the issue ourselves and study it, or simply continuing to troubleshoot it on your own with what guidance we can provide (as you have been doing up to this point). It seems like the first two options aren’t on the table for you, so with the latter option we forge ahead - no worries, we’re more than happy to help in that way.
I’d say raise a support ticket with Cloudflare - their team should be able to help you troubleshoot their service for potential issues. Unlike Caddy, as a massive enterprise with a paid service they also offer pretty good private support for their free tier, which I’ve taken advantage of in the past; last time I had to contact them I was having issues with SSL negotiation to some of their proxy servers, and we got into the weeds with packet captures and some low level network troubleshooting, it was pretty nice.
I’d especially recommend it in light of this:
The further information that this is all happening on a single domain, and the rest of the subdomains in the same zone are working fine is very confusing. It’s probably not a zone-wide issue, then.
Tell them simply that you have an ACME client (Caddy v2) that uses their API to solve DNS challenges, and a single subdomain is producing SERVFAIL results while other subdomains are working fine. Then ask if they can provide any assistance in troubleshooting this rogue subdomain.