I suspected it might be that (and tried to find a way to get at Deep Harmony code). Deep Harmony will use 'source controls" to send information to the pseudo roku player and I think usually translate to an ir signal - but perhaps Harmony also had ip control (I used it years ago but is now pretty obsolete).
What do you use Deep Harmony for may I ask? It may be possible to use ip controls or other approaches in a similar way to how RHEOS controls and switches other AVRS.
Unfortunately Deep Harmony is a black box and I fear may be incompatible with 2 way control (the difference from RHEOS 0.8.6). It will send control codes that will be reflected as changes to the zone control of ROON and that may well interfere with input swiching I dont honestly know.
Please explore how it works without Harmony on and perhaps let me know what else you find is a problem or what’s missing in the control of the 40N. Either I can work on disabling 2 way for a situation such as yours or free you of the harmony box. It should switch to HEOS whenever a stream starts from RHEOS irrespective of whats playing.
If you use Harmony for controlling other devices etc I can understand you dropping RHEOS.