Abdicating in favor of Prince Thomas didn't revert Khan's announcement. He wasn't a member of the Global Army anymore, and the same went for his organization.
Theoretically, that would prevent Khan from relying on the Global Army's structures, including Nott Station. Alternatively, he would have to go through many political hoops and send various formal requests to make use of them, just like any alien organization did.
However, Khan was a special case. His announcement didn't remove his status as a Prince nor the Nognes family's backing. Actually, killing Miss Christen had reinforced it, uniting all the Nognes factions behind him, at least publicly.
Khan's Lordship also was something the Global Army couldn't ignore. The shadow of the Empire was too terrifying to disrespect, making him an exception among exceptions. Khan wasn't a human politically, but the Global Army wouldn't refuse most of his requests.