All I can think of for the moment is that perhaps you have exceeded some limit regarding the number of email accounts and/or storage allocations.
The email account in question: Is it an older account or perhaps more recently created? How many accounts, emails, and associated storage do you have?
Even if the settings on that account are identical to the other accounts, I would try changing the settings to some other values, save the settings, and determine if the new setting(s) is/are working. If so, go back and reset again back to the desired configuration. Idea being that the premature deletions are due so some bug or corruption. A "do over" may fix the account's deletion policy.
Failing that then contact Mozilla.