the order looses no rights to any ship ( no matter if you re a player-faction-member or a non-playerfaction-member )
they have lost the battle of minor ( but it wasn t a competition, but part of a scripted event made up by the factions involved there )
they gain a few new structures that explain their new situation.
all in all - little changes in the small scale for the order. - large scale - the order may like to RP differently - but thats up to the player himself