It may be as simple as swapping barrels. With the .40, 9mm, and 10mm guns. At worst, you may have to buy a new top end. (With most Witnesses, the 9mm and .40 mags are interchangeable, if they are made for the proper frame size.)
With some Witness models, the .40 and 9mm have the same barrel diameter, and the barrels is built so that the extractor and headspace are correct when the barrel is changed. (I have one like that, but mine came with a separate top end; I can just swap barrels, too.)
When you talk to EAA again, ask about it. It may be much simpler than you might think.