1) Since you are familiar with what a hot leg is, are you comfortable in "rolling" 1 or 2 of the flickering lighting circuits over to other known working single pole breakers of the same amperage in the main panel or middle sub-panel?
We need to determine if the lighting flickering is being caused by one hot phase or both of the hot phases and if the flickering will follow or go away when "rolling" the lighting circuit or circuits over to the opposite phase.
Keep in mind that the lighting circuits only reside on (1) one hot leg, yet the H2O heater takes 2 hot legs. The $64K question is, does the flickering stop or does it follow when a lighting circuit is "rolled" from 1 hot phase to the other hot phase?
As you are probably already aware of, your main panel contains 2 hot phases which originate from the transformer and tandem thru the meter and onto the lugs on the main panel. The double pole feeder breakers to the other 2 sub-panels also contain the same 2 hot phases.
2) If you have a "clamp-on" amp meter and when the home is under Full Load (all possible electrical items in the ON position).......ie..........every light, TV, radio, microwave, dryer, washer, pumps, etc are all in the ON position. In other words, fire up every possible load in the home simultaneously. Then the clamp-on amp meter can quickly confirm if the 2 hot phases are close to being balanced. Both phases won't have identical amps under full load but should be somewhat close.
The amount of amps on the neutral service entrance conductor at the main panel will be the difference in amps of the 2 hot phase amp measurements..........ie........ Highest Hot phase (-) subtracted from the lower hot phase will = the total neutral current under Full Load.
3) There is no hierarchy as to the position/location of a double pole circuit breaker in any panel. The voltage (120VAC each side) is evenly distributed on both sides of the hot bus bar from the main breaker thru the hot bus bars and onto to a double pole breaker. What does matter is if the phase amps are close to being balanced when under full load.
Reply back to me when you have an opportunity and we can take it from there............Thanks...........Kevin:)