Say if I had 100% chaos converted to aether damage, would that convert the damage from all sources like item procs too ? Like the entropic coil ring proc is a chance to deal some chaos damage, would that then be converted to aether ?
If you’re referring to the transmuter for AAR, no. That only affects AAR.
If you’re referring to conversion from items or passives like Albrecht’s Duality, yes. All damage that starts as chaos becomes aether and is then modified by aether modifiers.
Thank you 
We really need a “All there is to know about conversion” sticky’ed somewhere, these questions pop up once or twice a week.
Hijacking the thread, I have played for 2 years but still don’t know that: does conversion affect retaliation damage?
It doesn’t.
AFAIK nearly all retaliation is piercing and non-physical based, I’m not sure there are any physical based retaliations so you wouldn’t be able to even test this… but as a test I tried to make a mod with convertible retaliation, doesn’t work.
Also hijacking it, can double conversion happen if I convert A to B through a skill and then B to C through an equipment?
(Game Guide mentions: The order of events for Conversion is as follows: Base Skill > Skill Modifiers > Conversion on the Skill or Transmuter > Conversion on Equipment and Buffs > Equipment, Auras and Passives)
Counter Strike offers Physical Retaliation nowadays.