As long as you can justify the fact that you were unable to take the leave to your boss, you shouldn't have a problem and your boss should fight it for you if he's got any kind of spine.
People in management positions have to realise that it takes time to prepare for deployments, which means you can't take leave, then you have to deploy, which means you can't take leave, and when you get back you have to go to work because someone else in the office is deploying, which means you can't take leave.
Justification is the key, along with a formal letter if necessary. It made things all okay for me after 6 months in Kosovo, along with an underlying threat to go public... now that the public are more on our side than they were 10 years ago, it might make it easier again.
Good luck.