Cabe writing:

The situation at least is clear:

• Because there was "the boy" (an altar boy) attending, we know a Mass was being celebrated. 
• The slip must have occurred when the two of them were near the chalice. 
• The most likely and the worst time that this might have happened was during communion itself.  Then it is usually the priest who holds the chalice containing the consecrated host.  As he gives communion, the altar boy holding a salver* is close enough to bump him or hit his arm. 
• Yet we know the boy probably did not jostle Father Flynn because Eliza says "They say it was the boy's fault" rather than "It was the boy's fault."   Further evidence is found in the aunt's comment ("I heard something") that shows there was gossip and rumor about it.

The question remains, was there anything in the chalice?  Most likely there was, but Roman Catholic doctrine is clear on this point.  While the implication of Eliza's comment involves the horror of spilling god on the  floor, doctrine explains that this is impossible.  The very instant the miraculously transubstantiated blood and body of Christ is not part of the sacrament of communion, blood instantly becomes wine, body instantly becomes  mere wafer.  So in that sense, of course, "it contained nothing."  However, the chalice itself, because it had been dropped, would have to be re-consecrated by the local bishop before it could be used again--in other words, even if it had not  been broken, it would have become at least temporarily dysfunctional.

I can't help noticing Joyce's repetition of a word, though.  It begins in the boy's thinking that precedes Eliza's account:

                                   We waited respectfully for her to break the silence: and after a long pause she said slowly: --It was that chalice he broke...

In the chalice, ostensibly, was God.  In the silence...was nothing.  As in, "it contained nothing."  We should think about this on various levels.  Fr Flynn dropped and broke the chalice so that a reconsecration had to occur. 

*Salve r= a tray, comes first from the Spanish salva, "originally foretasting of good to detect poison," and before that from the Latin salvare, "to save."  [American Heritage Dictionary, 1970]. The usually golden tray is an object intrinsic to the celebration of Mass in Dublin, 1904.