So, did we actually gain anything for our UEFA co-efficient number by beating Lyon? According to the text copied below, from the UEFA web site, it would seem our win at WHL or draw at Lyon didn't gain us any points. 
Advancing past Inter to the 1/4 finals seems to have only granted us a single, meagre point and would appear our 3-0 win doesn't earn us the two points granted for earlier, less important group wins. Seems strange. Anyone know better?
UEFA Europa League points system 
First qualifying round elimination – 0.25 points 
Second qualifying round elimination – 0.5 points
Third qualifying round elimination – 1 point 
Play-off elimination – 1.5 points 
Group stage win – 2 points 
Group stage draw – 1 point
Since 2009/10, clubs have been guaranteed a minimum of two points if they reach the group stage and are awarded an additional point if they get to the quarter-finals, semi-finals or final.
*Penalty shoot-outs do not affect the calculation system.
Taken from here: 
http://www.uefa.com/memberassociations/uefarankings/club/index.html