Yes, that's fine. There's no reason at all why you can't say that. The first 'for' belongs to the phrasal verb 'been looking for', while the second is a preposition of time belonging to the phrase 'for over a decade'.
In spoken English, they wouldn't even sound like the same word. The first 'for' would be in its full form, while the second would have its vowel reduced to a weak schwa sound.