Hi,
That is odd. I recall having issues with Cloudflare as a proxy. Not that issue (I was getting 525, which was a different issue). I haven’t come across a 523. Perhaps others have, though the lack of replies suggests perhaps not.
I’m not sure how you could debug since if the request is not even getting to Fly, it wouldn’t be in their log 
I assume Cloudflare’s raw logs are Enterprise-only but that could be worth investigating to approach it from their end.
If it is something to do with TLS … another option to look at could be TCP pass through, where your app handles the SSL. It’s a bit of extra work but you would probably add the cert to the app (origin, in Cloudflare-land) …
… and could then securely connect to it.
In your fly.toml you would remove the http/tls handler. That would take the proxy to some extent out of the way (at least that part of it):