So I have found at least one bug in the plugin which could account for some of the confusion. The bug appears in instances where a single device address is shared by multiple Indigo device IDs (think multisensor). For these devices, the neighbor list could be incorrectly set to the last queried device with a valid neighbor list. A little explanation might help get the point across. Think of an Aeon Multisensor with the z-wave address of 2:
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last_good_list = [2, 4, 5, 6, 7]
humidity id = 12345671 address = 2 neighbors = []
light id = 12345672 address = 2 neighbors = []
motion id = 12345673 address = 2 neighbors = [3, 4, 5, 6, 7]
temperature id = 12345674 address = 2 neighbors = []
When iterating through the devices, if the motion device was queried first, the neighbor list would be correct. But in instances where any of the other sub-devices were queried first, the neighbor list would be the same list as the last good list. I'm working on a fix now and taking the opportunity to fix a few other things with the codebase.