Flexmail use its own database to store mails located in independent mail accounts created on the mobile device. So it is only possible to synchronize mails stored under "Local folders" in Thunderbird since they are synchronized in "ActiveSync/E-mail Outlook" mobile account which is shared between Pocket Outlook and Flexmail.
It is not possible to synchronize mails located in independent mail accounts in Thunderbird (with their own Inbox, Sent,... folders) and in Flexmail mail accounts (different from "ActiveSync/E-mail Outlook").