It's important to realize that the term Khan is more general than most think. It means, most simply, "ruler" or "commander."

Differentiate that, then, with the title of Khagan (alt. Qagan), the title adopted by Ogedai Khan from Turkic and which can generally be understood to mean "Khan of Khans," or Yehke Khan, meaning "Great Khan."

The ability and propensity to have multiple Khans under a single Great Khan (Khagan) far predated the Mongolian Empire, and such titles were used by not only them, but its predecessors the Göktürk Khaganate, the Rouran Khaganate, and the Xiongnu Empire.

It's likewise important to note that while the Steppe Confederations were truly and existentially terrifying hen they were united by a Khan of Khans, such as Borgijin Temujin, that was typically the exception, rather than the rule of the Steppes - as indicated by the fact that we commonly refer to them as confederations, the had the tendency to shatter into their component sovereign tribes/peoples when a sufficiently strong Khan was not around to hold them all to his will.

Some to, perhaps, more directly address your question, let's actually pull back a bit and look at a couple of other on-again-off-again empires and the titles they'd use in pretense... First (a personal fave of mine), China: Prior to the Qin Dynasty's political unification of China in the 3rd c. BCE, the term for the ruler of any one of the several states was 王, most commonly iterated as "king", but likewise associated with "prince" as well. Once the First Qin Emperor, Qin Shihuang, united the empire, he took the title of 皇帝 (Huangdi) to differentiate himself and elevate himself above the mere "princely" and regional 王's. Nevertheless, the title did not die out, but instead lived on both within a given dynasty's imperial household - bestowed to the Imperial Princes - but also in times of disunion and civil war, when regional warlords would variously declare themselves either Emperor or Heavenly Prince (天王) in pretense. In the absence of a single uniting ruler, the terminology and titles of that rule would nevertheless be claimed in pretense by those seeking to using that assumed legitimacy to their advantage.

The same thing goes for much of European history. The Roman Caesar not only had 2 official holders at a time after the East/West Split into the Tetrarchy by Diocletian in the late 3rd c. CE, but even after the total collapse of political power in Rome, the title was retained by the Emperors of Constantinople. Not only that, but even much later, many Emuopean warlords, monarchs, and regional rulers would hold claim to the title: The Kaisers of Germany, the Tsars of Russia, Bulgaria, Serbia, etc, the Kayser-i-Rûm of the Ottoman Turks... just to name a few of the more notable uses.