As long as you're not planning to leave anything there, you can't violate export restrictions. A manufacturer (or its jurisdiction) can't restrict your use of a good. Otherwise you'd better check if your underpants are Made in USA!
The exception would be a software license but I would expect that its restrictions are around export. The airspace above a country belongs to its jurisdiction without vertical limit (well, there is an informal agreement on the Kármán line at 100km) so if there were restrictions, no airplane could overfly Iran. In reality, a lot of airlines operate scheduled service to Iran using the standard Airbus/Boeing airplanes.