The price on January 4th was around 285 USD and they lost ~18K BTC or ~5.1M USD at the time. They decided to cover the loss in BTC for their customers, they didn't have any option but to absorb the loss and respect the BTC balances of their customers in the exchange accounts.
But did they really had all those coins? Or were their books unbalanced and operating on fractional reserve, so that if everybody withdrew at the same time they wouldn't be able to honor all of the coins. And even if they did, how to recover their losses?
Answer: crash the price. At the bottom of the crash on Bitstamp 152 USD, getting the 18K back was ~2.7M USD, that is almost half the amount of the original loss. Obviously I am just speculating, but they definitely benefited from the crash, that conveniently happened right after they "lost" all those coins.
This unregulated market definitely needs a decentralized trust-less exchange, so we don't have to guess.
Price were crashing already before they were backup and running.
Even worse, maybe they were dumping their customers coins on other exchanges and buying them back lower before reopening their exchange.