This is one amazingly cool effect that I've only ever heard being done on the FoxRox Paradox TZF (no longer available) or in the studio with deep stereo flanging. Plus, this baby does a spot on Leslie, Vibrato, Chorus, Tremolo, Undulator and a bunch of other studio grade effects listed below...
Setting Notes: After a lot of initial experimentation, I was unable to get this effect because the deep cancellation effect on songs like "House Burning Down" and "Axis Bold As Love" used negative through zero flanging which is a hollow sounding effect, compared to most typical mono flangers which are positive. The ModFactor is 2 channels with the left channel being positive and the right channel negative with the flanger patch. So after talking to Dan Gillespie, Sr. DSP engineer at Eventide, he came up with a work-around suggestion on how to pull it off (Thanks Dan!). He suggested for a mono setup, to run my guitar signal into the left channel mono side and then run the output from channel 2 which would be the negative side out to my amp. Then just set the flanger type to Through-Zero and other settings set to Envelope to get the deep cancellation effect along with some tweaking on speed, depth, etc. I also used an expression pedal to go from full audio to the cancelled effect fading out and back in to the full flanging sound level. As a result, Dan mentioned that he's put this on the list for a future update so as not to have to do the work-around along with adding a realistic sounding Uni-Vibe patch which many, including myself have been asking for. These guys are really on the ball.
Also, to get the full "House Burning Down" or Axis Bold As Love" effect, you need to have a good amount of distortion or fuzz going into the ModFactor to really hear the deep cancellation stereo flange effect. The ModFactor was also ran into an Eventide TimeFactor delay set on patch 5:1 which is a cool Red House-Echoplex type patch setting. I must say that the sound quality of these Eventide units is just pristine and are top studio quality, not like a lot of the fake sounding modeling stuff out there. Instead, these really sound like full analog effects that are then further polished to an ultra sheen as if they were professionally mastered while playing live!
Reverse Strat >Boss TU2 tuner>Way
Huge Fat Sandwich Harmonic Distortion Satchurator>Eventide
ModFactor+Expression Pedal - Patch 4:2>Eventide TimeFactor Patch
5:1>Marshall JCM 800 50 watt Split Channel Reverb Combo w/ Celestion
Vintage 30 Speaker. Recorded with Boss BR864 8 Track Digital Studio
Mixer using a Shure SM48 Mic placed at the speaker's edge about 3