Actually it's very easy, and you don't even need to add a second folder. Just name the lensflare blinker texture whatever you'd like to name it (for example lets say lensflare.tga) and drop it into the existing folder.  Now all you have to do is go into the hardpoint of the ship you'd like to change and scroll down to the blinkers.  You'll see a line towards the end of each one:
"scripts/Custom/NanoFXv2/SpecialFX/GFX/Blinker/Blank.tga"
rename "Blank.tga" to "lensflare.tga" (or whatever you named it) on all the blinkers you want to change.
That should do it.