Where are you getting your 2.1 million figure? It was 913,000[0].
Combined with 699,000 votes for Clinton/Kaine from suburban Cook County[1]—whose voters seem to have been unaffected by this breach—you get the 1.6 million number reported by AP for the county[2].
I'm pretty sure this is a reference to the "vote early and vote often" phrase that is typically correlated with Chicago, and especially with the Democratic machine politics.
Someone else in this thread made a similar joke and has an all too literal response. I'm starting to think our irreverent sense of humor for our city's politics doesn't translate well.
Source: Chicagoan. And I found this hilarious.