One problem is the loss of a third of his water. He used up the hydrazine fuel left in the lander - it was the only hydrazine he had available. There's only one other MAV on Mars, and he needs to leave that one intact to be able to leave Mars. There is no other source of hydrazine.
The Martian, Ch. 15:
As for water supply, I have 620L remaining. I
started with 900L (300 to start with, 600 more from reducing
hydrazine). So I lost almost 300L to sublimation.
The other problem isn't completely s-p-e-l-l-e-d out in any one place in the book, but it's the lack of Earth soil bacteria. He only had a small amount of Earth soil to start with, and after the accident all of the enriched soil he made was sterilized. In hindsight he probably should have kept a small sample of the enriched soil stored in a safe place, but nobody can think of everything.
The Martian, Ch. 14:
With a complete loss of pressure, most of the water
boiled off. Also, the temperature is well below freezing. Not even the
bacteria in the soil can survive a catastrophe like that. Some of the
crops were in pop-tents off the Hab. But they’re dead, too. I had them
connected directly to the Hab via hoses to maintain air supply and
temperature. When the Hab blew, the pop-tents depressurized as well.
Even if they hadn’t, the freezing cold would have killed them.
Potatoes are now extinct on Mars.
So are earthworms and soil bacteria. I’ll never grow
another plant so long I’m here. (incidentally, this is the only mention of earthworms in the whole book)
Later, he finds out that some of the soil bacteria had survived and was replenishing the soil. But by then he was hard at work on the new rescue plan and didn't have time to go back to farming.
The Martian, Ch. 17:
There's still soil everywhere. No point in lugging it back outside.
Lacking anything better to do, I ran some tests on it. Amazingly, some
of the bacteria survived. The population is strong and growing. That's
pretty impressive, when you consider it was exposed to near-vacuum and
sub-arctic temperatures for over 24 hours.