Hurk after third or fourth thought if the conductors are running in the same conduit
to and back in the same conduit, well you are probably right. Just seems like there
should be something wrong there, would the neutral be affected in the J. box ?
Yep it's a hard one to grasp and took me playing with a clamp on amp probe to get my head wrapped around it, the neutral does not even come into play here, if all the current that flow into a raceway is returned by the same raceway any current fields are canceled out because current flowing to the disconnect will be 180 deg. out of phase with the current flowing out of the disconnect, even if there is neutral current in the circuit it doesn't matter since the only thing that matters is the current caring conductors in each raceway must mirror each other.
The same in the junction box, all current carrying conductors are in close proximity to each other (unless the box is huge) and will still exhibit the same effect, and since the neutral is in with the fed to the junction box and leaves to the load with all current carrying conductors the same thing happens.
Next time your in a disconnect try clamping a amp probe around both line and load conductors of a circuit, you don't even have to get the neutral in it to prove this, just the line and load, but you will not see any current on that amp probe, at this point they don't have to be in the same conduit since the theory is the same.
Another way to think of this is lets say you have loose open conductors with a load on them that you could bend tight and insert into the coil of an amp meter, do one at a time or all of them since each just runs through the coil and back out through the same coil it cancels out the current field, this would be just like the conductors to the closed disconnect then back into the same raceway.