As per the guide the flashing indicates the module is already programmed and can not be programmed again.
If i'm not mistaken OB-3471v is an orbit start and if the battery was dead it is much more likely there is a problem with the starter and not the module.
Now i can't find a manual for the orbit start version but if it's like the canadian tire version (CT-3471) they have a tendancy to lose their programming if the battery goes dead or voltage spike and if it has the dual data ports (RS232 and D2D) there is an option in the programming tables for Fortin and 1 way communication (default is D2D 2 way)
But before going that far into it,
Does the remote respond?
if so will it go into reservation mode?