If I am running a 2 inch pipe at 20PSI of cooling feed water and I run a bypass pipe of 1/2 inch diameter in parallel for 6 feet and then rejoin the 2 inch pipe, will say, a 5% reduction in flow through the main feed pipe be reflected by the exact same 5% reduction in the bypass pipe flow?

 

The change will not be exactly the same percentage for both branches but for a 5% reduction it will likely be close enough. The pressure drop for the two branches will be equal at any flow rate. At the lower flow the pressure drop will be lower. The equation for each branch is:
delta P = f * delta (v^2) * L/D where
P is pressure, v is velocity, L is length, D is pipe ID and f is the friction factor. For each branch L/D is a constant. f is a function of velocity (and other parameters that will not change for this question). Over a small change f won't change much. Over a large change f may change significantly and not in the same proportion for each branch. It depends on the velocity, pipe type, and fluid properties.