This is what I've gathered from my own experimentation and from going through some of these forum posts:
Nodes:-
There are 4 types: Normal, Pure, Dark and Unstable.
Dark - Generate flux, which is liable to spill over into nearby nodes, rarely seen below Dangerous flux levels.
Normal - Do not generate flux, but will get flux either from nearby nodes, or from player actions. Will generally take action on it at moderate levels of flux.
Pure - Do not generate flux, but will get flux from nearby nodes or player actions. Always seeks to be completely free of flux.
Unstable - Not sure. Possibly similar to Normal, but generates low amounts of flux on it's own.
As far as I can tell, this has no bearing on HOW the nodes clean themselves. The common method is to spawn wisps (any flux type), but it can cause other effects. Excess of the Weather aspect can cause unnatural rain, for example. Pure nodes will continue to produce these effects until they are free of flux. They do NOT (as far as I know) spontaneously remove flux from themselves.
Effects of flux (i.e. flux "materialising" back into the word) have been observed as:
- Wisp spawning.
- Rain.
- Giant Spawning.
- Witch Spawning.
I'm fairly sure that there are others, but I haven't seen them myself.
The only method I am aware of of "cleaning" a node is to use bees, specifically those with the "purify node" flower requirement, obtained from the Pure species. These will "eat" flux, rather than spreading flowers or pollinating trees. The resulting crystalisations are deposited in the bee's house and can be either used directly, or converted into essentia phials.