The house we bought has two blue cold water pressure tanks, both with bladders, and the system is set for cut-in at 50 and cut-out at 70. We noticed a tiny pinhole leak in a tee connection close to where the well line enters the house - so we turned off the pump and drained water from the tanks enough to allow work on the tee, which is about 5' off the floor. Tee repaired, we cleaned and changed the sediment filter, put in a new filter, and then checked the bladder pressure while the pressure was off the water tanks. Both pressure tanks bladders were charged to 38 pounds rather than 48, only because it seemed like it was taking forever to do that. Both of the tanks, before charging the bladders back up, were at about 24 pounds each (the tanks are in tandem, one larger than the other). Refilling the system was normal, and we let the water and air blow out of lines through the house. However, we now have a situation where, as the pressure drops before the pump cuts back in, there's very little water pressure on the second floor (tanks are in the basement) so the bathrooms/showers are an issue. Tank pressure seems fine, and the 50-70 in and out seems high to us, but that's how the prior owners set up the system, so we've never messed with it. Until now. Help!
I think you have two completely separate issues that you became aware of at the same time, and which are mostly unrelated.
Improperly set system and air pressures in bladder tanks.
A note - the higher the system pressure, the less water storage (drawdown) in a bladder tank. So you might get better performance from a 40/60 or 30/50 setting.
You are also at risk of damaging the bladders by underfilling the air for the pressure you have set on the water side. The bladder becomes much more distended than it's designed to be, and lots of water simply sits in the tank with the effective volume of the tank greatly reduced, since the first water to enter the tank is raising its air pressure from your too low setting to where the pressure switch is set, and shrinking the air bubble to do that.
Low pressure on the second floor bathrooms is probably from a blockage.
Pressure due to elevation is 2.3 feet per PSI, so pressure on the second floor due to elevation is probably not really the issue (might be 8-10 PSI less than the basement in a typical house) and of course it worked fine until you drained the system; so it's not "really" pressure loss, in the sense of the pressure in the pipes - IMPE it is often the case that when you drain and refill a water system "crud" (usually harmless, but unappealing, deposits from the water) in the pipes gets knocked loose with all the bubbles passing through and will plug shower heads and aerators - that does cause pressure loss OUT of the showers and sinks. Try removing shower heads and aerators, cleaning them, and blowing the pipes clear without having them in place.
I would suggest draining the system again, verifying that the air pressure is still 38 (if not you may have a leaky bladder) and resetting the pressure switch to 40/60 (with a typical pressure switch, be sure to turn the pump breaker off before adjusting.) Then remove all showerheads and aerators, repressurize the system, and blow the pipes clear before reinstalling the cleaned showerheads and aerators.
We have the answer - Talking with the well/plumbing company that we had replace a jet pump in a prior home years ago, as he heard the issue he offered "just what filter cartridge did you replace?" It was a sediment filter, and he asked whether I might have replaced it with a carbon filter instead, and that if I had, the pressure issue might be caused by much slower permeation of the carbon filter accounting for the high pressure in the first tank and the lower pressure in the second. Voila - perfectly correct. Changed out to sediment cartridges (the carbon filters were handy and there while I was working - my bad in just slapping them into the filter), reset the bladders, refilled the system - perfect!