i'm sure they will be fine after a good slow charge.....hopefully.
the same thing happened to my ezrun 150a esc back when i converted a savage x 4.6. the flightmax 3s lipos puffed about the same amount and they were almost back to normal after a couple cycles on the charger. almost 100 cycles later, the packs are still good but are prematurely aging compared to my other lipos.
just give your lipos a few cycles on the charger and hopefully, they will go back to normal.
edit: the dead ezrun is what motivated me to get a MMM.