Cubatabaco, the government-run company in charge of cigars, half-owner of Habanos SA, along with Altadis SA, promptly began a campaign to have General Cigar's trademark revoked and numerous legal battles ensued that were partly resolved on 19 June 2006, when the U. S. Supreme Court denied Cubatabco's petition. As a result, the February 2005 decision of the U. S. 2nd Circuit Court of Appeals (Docket #04-2527), which confirmed General Cigar Companys exclusive ownership of the Cohiba trademark in the United States, is final and is law of the case. The General Cigar-made Cohiba cigars now have a disclaimer on boxes that they are not affiliated in any way with the Cuban brand.
However, the United States government, in an amicus curiae brief filed in the Supreme Court, acknowledged that Cubatabaco could request U.S. government permission for judicial protection of the brand from the Department of the Treasury's Office of Foreign Assets Control, which administers the U.S. blockade. Cubatabaco has stated that they intend to pursue this course of action.
The above is from Wiki.
I'm no lawyer, but I think the judge basically said to Cuba "dude, you're and embargoed nation and have no rights". When/if the embargo is lifted, and free trade is the desire of both nations, it's just my opinion that the US gov't won't say, "never mind that you could not register a trademark, but too bad you didn't register". Time will tell
Regardless of what the final resolution will be, the possibilities are endless.