I recently changed factions due to joining an alliance guild on another server and stood in my bank thinking if the tabards in my bank that had been changed to alliance equivalents would count again for Twenty-Five Tabards. To my surprise they did. It's hard to get proof of this but I can assure you it will work, so if you intend to faction change buy/equip every tabard that changes. Tested with Argent Tournament/PvP/Battleground tabards and it worked with each and every one of them.
Sorry if this is a repost, didn't find any with search.