Can I increase retraction length on an E3D v6 beyond 2 mm if I have a really long Bowden tube?
Yes, you can increase retraction past E3D's max 2&nbsp;mm recommendation to compensate for Bowden tube stretch and slop. The reason for the recommendation is that jams will occur with most all-metal hot ends if you pull molten filament up into the cold zone. Any molten filament that enters the cold zone rapidly cools and hardens and sticks to the walls, very often forming a jam. 

So, the requirement is to keep your retraction distance at the extruder less than 2&nbsp;mm. Additional retraction travel that is absorbed by the Bowden tube and not seen at the extruder is fine. I personally run 2.5&nbsp;mm retraction on an E3Dv6 Bowden system without any issues.