Kypto and the rest of the Legion of Super-Pets do not appear in Crisis on Infinite Earths. If Wolfman and Perez thought it was all too silly, I don't know. Perhaps we were spared a gruesome death for the Dog of Steel. (He'll get a proper Bronze Age goodbye soon, I promise.)
At least Ambush Bug remembers, and in his "History of the DC Universe", he made a point of paying tribute to the Super-Animals left at the pound that day. So sing a song in his honor, Krypto was his name-oh. -Whine-
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Ouch.