Dead easy, just swap out the trucks. You usually have to break the coupler mounting boxes to get the 2-rail couplers off, although if you are extremely careful and have just the right tools for leverage, you can pry them off intact. It doesn't matter anyway, new mounting boxes are cheap and any 2-railer you sell or swap the parts to will have plenty of them in his parts box.
You'll have to do some minor rewiring for a caboose, but Atlas makes interchangeable caboose trucks with the center roller already mounted, so once again, it's easy. The electrically isolated wheelsets are for 2-rail, not 3-rail.
On large, modern cars you need to check the length of the coupler shanks. The really big stuff (89' flatcars and I don't know what all else) has couplers with longer shanks and you will have to get the correct truck/coupler assembly for the car. The big Hy-Cube Berwicks may be in this category, I'm not sure. Again, no big problem, just call Atlas and they'll tell you the right one, or you can look up their online parts diagrams if they have one for your particular car. The big Hy-Cube Berwicks may be in this category, I'm not sure.
Another solution, if you have excess 3-rail rolling stock of the same type, is to just swap out the whole chassis and sell the donor car as a 2-rail item. This is easier (and cheaper in the long run), but ties up more capital until you can move your inventory.
