I'm not sure I follow you here. Firstly, yes you will lose your iPhone apps if you wipe your hard drive clean, however you can re-download them again for free using the same Apple ID. Although re-syncing your iPhone should restore them in any event.
However, it seems you want to reinstall OS X because Windows XP won't accept your license code under Parallels? That won't fix the problem. There's very very very rarely a good reason to ever reinstall OS X, and this isn't one of them. Presumably, the update to Parallels triggered Windows to think your hardware has changed and wants you to reactivate it. You should contact Parallels customer service and check with them since their update triggered the problem.