Chrysalis detects the Atreus by its USB Vendor and Product ID. If those remain intact when flashing a QMK firmware onto it (and as far as I remember, they do), Chrysalis will be able to detect the keyboard. However, it will not be able to talk to it, and will guide you to the Firmware Update screen.
It is technically possible to teach QMK to talk the same protocol as Kaleidoscope, and work with Chrysalis just as well as Kaleidoscope does, but there will be certain incompatibilities (ie, keycodes are different between QMK and Kaleidoscope, for pretty much all keys outside of the standard USB keyboard set) that make this impractical at this time.