Q: When a bishop celebrates mass, why does he remove his zucchetto at the beginning of the eucharistic prayer until after communion?
A: Apparently, it is removed because of the real presence of Christ in the course of the mass. It parallels the custom of removing the zucchetto in the presence of the exposed Blessed Sacrament, even in processions, and in venerating or blessing with a relic of the true cross.
On Good Friday, the cross is treated as if it were the real presence of Christ. The liturgical texts speak of “adoring” the cross, and the proper gesture of respect for it is a genuflection – only on that day. When the bishop goes to adore the cross, he does it with head uncovered (no zucchetto) – another parallel to the real presence of Christ in the eucharist.
The custom has a couple of benefits for liturgical theology. It stays out of the question of when precisely the consecration occurs during the eucharistic prayer by having the bishop remove the zucchetto from the very beginning. It also draws a helpful distinction between the real presence of Christ in the tabernacle (usually present throughout the mass) and on the altar.
I don’t know enough about the history of the Ceremonial of Bishops to tell you when it originated, but that would make an interesting study.