The reply flags are not universally supported by mail servers, so some remove them when the IMAP account is synchronized.

Thanks for the explanation. Old messages still show the reply flag, so is there a way to reset the default so reply flags will show again on newer messages?

Are the old messages in a pop account or local folders? Are the missing flags in the same folders? Do you get flags if your start in safe mode? Hold shift while starting Thunderbird and continue in safe mode when prompted.