I have had this happen more than once. I know it can be frustrating. QuickBooks thinks that all your checks printed, but you know there are problems. Most likely the printer jammed. Sometimes it's because the checks were put in backwards or upside down.
This is an easy fix. Go into your check register and locate the checks that need to be printed again. Go to each check individually and do a right click with your mouse. Choose "edit check". When the check comes up on screen, mark the box "to be printed". It's a small box and is found on the right side below the signature line. Save each check again. Once they are all marked to be printed, and you have saved them all, then go to file (top right corner). Scroll down to "print forms". Slide across to "checks". Go through the process of printing and be sure to put in the correct starting check number. If any of your check numbers are incorrect, you can change the check number in your check register.