The upgrade didn't fail, because at version information in the CMS i see R59 properly at each display.
I only have remote SSH access to the Android boxes (I'm at 200km away from them), I don't see how I could interact with superSU.
As far as I remember, I ticked it to remember permissions forever for all the boxes.
Last time when I upgraded, I had no problems whatsoever, so I don't think it has anything to do with SuperSU by itself.
I unassigned the APK, and deleted it from the server, but the loop still continues. I restarted manually the app (with comands above), but still looping.
Note, the upgrade seems to be gone through well, but somehow the app thinks it has to restart itself over and over again.