Have you tried asking Fortigate about the truncation?
Are you trying to issue a fresh cert for the secure subdomain? Or, are you just bothered by the "account paused" error message?
In the last 2 years I only see 2 certs issued for that subdomain and those were last June and July. The most recently issued one expired 4 months ago. It doesn't seem like a domain name that is essential. Would using a different domain name work-around this problem until you can get help from Fortigate?
This rate limit is described here: Rate Limits - Let's Encrypt This rate limit is only imposed after a large number of consecutive failures for that specific domain name.