I think that trace cut is just to correct an output loading problem in bypass mode.
What does happen in this pedal in auto mode is that the filter is swept up, or open, by a control signal that is derived from the input signal. This signal tracks (more or less) the instantaneous volume of each input note. If for any reason the input signal is not large enough, or the rectified volume envelope signal is not being generated by it, the filter does not open up. The filtering in this design in auto mode is so aggressive that when the filter is closed it acts like a gate - no signal reaches the output. You say that you get a swept filter effect in manual mode so you know the filter is basically working and the problems must lie entirely in the auto side chain.
There are various things to look at in the auto chain. First the signal passes through an amplifier - 1/2 of the op-amp. The gain of this amp is set by the sensitivity control and you normally need it set around the half way mark. There have been instances of bad pots and a bad pot in this position could mean not enough signal ever reaches the next stage - to check the pot you can probably use a multimeter on the 2M resistance range and measure in circuit with the power off (the pot has no DC connection to the rest of the circuit). it might be best just to remove the IC while testing the pot. Turn the pot with the multimeter attached and try to see if you get a smooth change in resistance up to around 250K.
The output of the amp feeds a rectifier of two diodes through a cap. Check the cap is the right way around and the diodes are the right way round.
With the IC in and the pedal powered, check that pins 3 & 5 and 1 & 7 are at Vref (1/2 the supply). If they aren't the op-amps are not biased properly and won't work correctly.
The cathode of D2 should be biased to 1/7th of the supply - about 1.3V by the 150K and 22K resistors. The Attack pot could also be a faulty pot. Once the rectified signal makes it through the Attack pot it is smoothed by the 4.7uF time constant cap and drives the base of the transistor - collector should be at supply (about +9), base should be at about 1.3 and the emitter 0.6V lower at around 0.7V (with no input signal). The current drive out of the transistor emitter drives the control current input of the filter.
Once you have the auto working you might want to look at -
http://www.buildyourownclone.com/board/viewtopic.php?f=12&t=34270 to get the manual control to work properly.