Ya, if you use a recessed cylinder in a frame that originally had a non recessed cylinder, you must file the lug back .060. I have made several recessed 45 colt cylinders from recessed 44mag cylinders. My N frame 44 special was made using a 357 cylinder and as I had purchased a reamer and had an abundance of cylinders I made several.
To file a lug back I use a file that only has teeth on the edges.The teeth on the flats having been completely ground off. Then I glue a piece of stainless steel heat treating foil to the frame, by the lug. This keeps marks off the frame. It does take a bit of filing to remove .060 and you must get the portion of the lug where the frame is rounded into the cylinder window.
Turning the recesses completely off the cylinder would not be hard, but in reality if you want to go that route all that really needs removed it enough to clear the frame lug, so that is another option.
As far as the value of recessed cylinders goes. I bought a recessed model 29 cylinder just last week fir $48 including shipping. While they may not make them anymore, the actual market for them is getting pretty small as few people wreck their original recessed cylinders and fewer still actual work on revolvers. I cruise Ebay and buy parts that may come in handy
I probably have 20 odd cylinders and at least as many barrels.