You can file, but you ought to think twice about it, because you will have to file an an amended return when you get the second W-2. And unless your withholding was quite high on the second W-2, you will likely owe tax when you file the amended return.
So file an extension (4868), pay whatever tax you think you may owe (hard to know without the second W-2), and keep looking for that second W-2.
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