Sherles wasn't aware of Greevil's existence at the time, but he was still sure that there was a lot more to Cipher than its base in Orre. Considering that Ardos was happy to blow up Citadark Isle, it is clear that they still had other resources outside Orre, much like they did before they revived the Orre branch. Sherles probably didn't know anything about Citadark Isle, but that only proves that what he did discover about Cipher had to do with another region.
I'm guessing that Ardos went back to the region where the rest of Cipher conducted their affairs during the events of Colosseum. Orre was the ideal environment for the first Shadow incident not only because Evice was in a position of power, but because Team Snagem were based in that region. In the second Shadow incident, the Shadow Pokémon Laboratory from the previous incident must have been the main reason why Greevil wanted to revive Cipher in Orre.