R' Elazar says that one who eats a kizayis of cheilev bishogeg should write down the
exact quantity of which he partook, in preparation for
the rebuilding of the Temple, when he can be makriv a chatas.
The whole premise of this sugya (as explained by Rashi)
is that beis din enjoys the authority to change the size of
a kizayis.
How could beis din do such a thing? The very next
line in the gemara, a statement by R' Yochanan, says
that all shiurim are established by a halacha limoshe misinai!
Are R' Elazar and R' Yochanan engaged in a disagreement?
Good question. It could be as you suggested, that Rebbi Elazar and Rebbi Yochanan are arguing. Perhaps Rebbi Elazar is following the opinion of Acherim quoted later, who say that the Beis Din of "Ya'avetz" (Osnial ben Kenaz) established the sizes of the Shi'urim, meaning that the Shi'urim were forgotten and the Beis Din re-instituted them ("Chazru v'Yasdum"), as the Gemara explains. Rebbi Elazar is saying that perhaps Beis Din might reconsider what they re-instituted and decide that a different size is the more accurate size to that which was given as Halachah l'Moshe mi'Sinai. (For example, perhaps there will become revealed a different Kabalah to what had previously been accepted.)
Y. Shaw