Broadly speaking two major possibilities are (1) lack of continuity between the "tip" lug of the input jack and the "tip" lug of the output jack when in bypass mode, and (2) a short between the "tip" lug of the input jack and and some other unfortunate point (such as ground) in the circuit, when in bypass mode.
Assuming you have a multimeter or some other way to check continuity, remove the 1/4 inch plugs and ...
(1) put the pedal in bypass and see if you have continuity along this sequence: input-jack-tip-lug, footswitch lug 4, footswitch lug 9, footswitch lug 8, and output-jack-tip-lug. Bad solder joints, a bad footswitch, or even a broken trace could cause a discontinuity here. A general a re-flow of the whole circuit could be called for, or in checking this route you might identify a particular solder joint that needs attention.
(2) put the pedal in bypass mode and see whether there is continuity between the input-jack-tip-lug and ground (there are many places to access ground). It's not as easy to predict where this might short-circuit might be, but inspection of the *other* side of the PCB could be useful (and normally at this point we would recommend showing us that side as well). NOTE however that since the pedal seems to work when switched on, it's harder to imagine how this problem crops up. If for some reason the footswitch lugs 4 and 5 are electrically connected permanently, in bypass mode the input signal will be routed through pins 6 and 3 and 2 to ground. This is admittedly quite a stretch for an explanation, but sometimes foot switches are bad, or some short circuit has been made. The jumper between lugs 4 and 9 of the footswitch passes close to 5, so it could happen.
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