Auto-rebooking is not the best on most carriers. Generally one has to do what you did and either call in or deal with it online for those carriers which have online IRROPS (rarely to be trusted). The purpose of the auto-rebook is to assure that you have something as opposed to nothing.
On the broader issue, B6 does not have interline ticketing agreements with other domestic US carriers so your alternative here was either to reroute as you did or to cancel for a full refund and then purchase a DL ticket.