Why was Ash's Pokedex replaced?
In Season One, ep66 "The Evolution Solution" Ash and his gang are going to Prof. Westwood, who programmed the Pokedex, once he sees Togepi he says "Now that's interesting Pokemon" after Misty asks "You mean Togepi" he says "I've never seen another Pokemon quite like that". although this may lead to a plot-hole as with Ash's Pokedex had been upgraded to know Togepi, as in the question, it may not be so much a problem since the Pokedex itself said "there's not much data" to imply that Prof. Westwood though he didn't have much data but may have heard about species like Togepi and insert that little information he heard and the Pokedex Associate the information to Togepi.

Anyway, to the question, Prof. Westwood soon tells Misty "Yeah, and I'm updating all my research materials about the rarest legendary Pokemon!", so it is safe to say that is exactly the new Pokedex Ash received before going to Johto since Westwood said itself that he is currently in updating his materials as the early upgrade Ash gets not to contain expensive data on Gen2 Pokemon and only after that update Westwood worked on the next Pokedex Generation. (support @f1Krazy comment)



And the evidence for that (although it's in the Advance series its still evidence that Westwood discovered new information) is in Advanced Challenge ep4 "The Princess And The Togepi" the Pokedex has much larger information about Togepi than the first Pokedex.