Corrosion is likely the culprit if the handle has not been removed in a long time. There are swords that are double pinned. The custom came about to assure the sword was usable if an enemy some how at access to your sword and removed the mekugi. If there is a second mekugi, it will be evident as the handle would require removal for maintenance of the blade. The tsukaito would never bee wrapped over a mekugi.
You can try using a hammer and a block of wood to break the tsuka free. Light taps increasing with force to see if you can find movement. A rubber mallet will also not do any harm to the tsuba.