Yes, you would have to remove the inverts (although funny enough I had the one giant hermit crab that full strength CopperSafe could never kill. He stayed in the overflow. Lol.) Although it’s possible that inverts can be returned to the tank once all the copper is out, most people go into the idea of nuking the tank with the understanding that they may never have inverts again. But to be honest, most people who run a FOWLR tank, especially a larger one, usually have one or more fish that would eat inverts… So it’s a moot point to worry about them because they don’t have them to begin with.
Is it possible to take your rocks out one by one? Because if if it is the Spiorbid worms that are your concern, I’ll take my rocks out and with some needle nose pliers I bust them off the rock at the base and that kills them.