[Dovecot] Maildir and IMAP keywords

When a user in thunderbird toggles some flags like junk, spam or something similar dovecot appends these flags form a-z to the end of the file in maildir.

I have another application that also access the maildirs which gets really upset with these flags and ignore those emails.

Are there any other way for dovecot to store these flags to make it compatible with other softwares?