This past Sunday, September 16, 2012, I attended mass celebrated by an elderly priest. Present on the altar was a covered ciborium. At the time father consecrated the large host the ciborium remained covered, father uncovered the ciborium then consecrated the wine. After saying do this in memory of me, father covered the ciborium. Does the ciborium have to be uncovered for the consecration of its contents? I never witnessed this before.
The cover would not have to be off the ciborium for the hosts within to be consecrated. However, it is both customary and fitting that it be uncovered before its consecration. It is not necessary to uncover in order the “let the consecration in”, as it were. The consecration doesn’t work like that. But it is proper to uncover it before the consecration of the hosts, and then cover it before continuing with the consecration of the wine.
It sounds like, from your description, that Father may have gotten a little scrambled and uncovered the ciborium in the wrong order.
A priest should form a moral intention to consecrate what needs to be consecrated. What needs to be consecrated should be placed upon the corporal that is spread upon the altar. Since the priest has this moral intention, he does not have to be thinking specifically about every host in every vessel. Uncovering the ciborium, however, certainly reinforces the intention and reminds the priest about the hosts to be consecrated.
But, no, were the priest or deacon to omit uncovering a ciborium before the consecration, the hosts within would nevertheless be consecrated.