It should be possible to persist inbound and outbound message sequence numbers for restoring session after disconnect. Add settings similar to QuickFix ResetOnLogon, ResetOnLogout, ResetOnDisconnect, RefreshOnLogon (see http://www.quickfixengine.org/quickfix/doc/html/configuration.html#Session).
Use persisted settings if FixSessionSettingsProvider.resetMsgSeqNum() == false.