Should be an option button in the Replication set up. Default to 3857.
If things were that simple what would they need GIS people like you for? Just saying...
Well, actually it turned out not to be that bad. The workflow did indeed work perfectly, for a viewer and two SDEs and their child GDBs. However, I imagine this is a common workflow - where GIS departments would want file GDBs in web mercator for web viewers. But they keep SDE in state plane. It would be an area for streamlining the interface.
I have been using this workflow for years now and as you said it in not a big deal.
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