Given that the engines are stored in the remotes, it's pretty "iffy" when you start swapping stuff anyway. For DCS, I routinely reset the remotes so I don't have overlapping and duplicate engine numbers. I'm sure there's a "logical" method to keep them all straight, but it's not logical to me.
In addition, having 40-50 engines in the remote gets a bit confusing to find the one you want to run. I prefer to have the ones that are in use at the time in the remote and the others on the shelf just on the shelf. It's not difficult to add a new engine, so I just add them when I want to run them.