Don't panic. I had eggs shipped from Georgia to California and many had large air cells from being ruptured during shipping. I kept my humidity at 40% day one through 18 and 65% for lockdown and I had a 100% hatch. I would however do the salt test on your hygrometer just to be sure. You shouldn't need two of your wells full to get your humidity up to 45%. I use the Exo Terra reptile hygrometer and it reads 10% low of the actual humidity so I know when it is reading 30% it is actually 40% in my incubator. What kind of incubator are you using and what kind of hygrometer are you using?
