Here's my setup, a Killer Joe with a Dark Steel Sword and a Item Conduit coming out to a chest. In the Conduit Connector it's going Input/Extract with Advanced Item Filter in Extract mode and Fuzzy match for 75% damage. Problem is keeps extracting sword with 1506/1561 damage.

EnderIO-1.7.10-2.3.0.428_beta
EnderCore-1.7.10-0.2.0.36_beta
Minecraft: 1.7.10
Forge 10.13.4.1558

You got your filter backwards. It is set to pull out items with >=75% durability. You probably want to set it to NOT pull out items with >=75% (or 25%) durability.