I've considered having a .38 Super barrel fitted to my Colt LW Commander 9mm- and may yet do so in the future.
I also have concerns about the possibility of getting things mixed up- probably better if I just stuck to what I already have.
I have not found any downside to the 9mm conversion. Mine uses a different recoil spring, 9-10lb vs. 15lb for the .38 super. I also have a separate spring plug and guide for each. I use 9mm specific magazines, Tripp, Mecgar and Springfield 9 round.
I would suggest that shooting any ammunition out of a platform that was not designed to shoot that ammunition is probably not the best possible choice,