I don't see the problem here.. Why do you think you're seeing a deficiency? If there IS a deficiency at this point, it probably has everything to do with your pH level which should be 6.3 to be perfect. If you've just got some yellowing leaves underneath, I wouldn't worry about them at all - probably natural dying off because they're not getting any light.
Many growers do what is called lollipopping - trimming off all the lower vegetation when they do a scrog - but again, do this carefully. There was one grower here a while back who pretty much took off every single fan leaf and left their plants looking naked and abused. Lost the grow, I'm afraid! I would go ahead and do the defoliation you plan - but I don't think you really need to then wait to flip... the grow looks strong enough to tolerate both as long as you don't go overboard on the defol. Defoliate some today, wait two days, if the plant is ok, defoliate some more, etc... but go ahead and flip now if you want.
Good luck!