1. As to OP's question, he did not violate AA's COC because he fully intended to fly the F ticket when he purchased it. Yes, it's suspicious that he cancelled, bought Y and then applied a SWU, but it strikes me that the further out the flight is, the less attention this attracts. In any event, I don't think that AA could ever not refund a refundable ticket. It could and might void a SWU, close an account and so on. Hopefully if AA takes action, OP will be able to ultimately explain.

2. As to expensing tickets after purchase but before flight, it is really bad practice for a company to prohibit that when the employee is using a CC for which he is on the hook. At current rates, fronting money is negligible. But, if you work for a company which goes belly up, unlike wages due which are a super-priority, the funds you have "loaned" your employer are a good old-fashioned unsecured debt and you won't likely see much if anything of them. Either use a corporate CC which is paid by the company or issue individual CC's which the employee can use for hotels and the like, but for which expenses such as airfare are stripped off.