First, that is a dinosaur or a plan that only allows changes twice a year. The reality is that the plan should be changed to allow changes in the deferral amount at any pay period.
Now, as to your situation, the employer was not permitted to take out deferrals starting in September. Since you are still within the same calendar year, I would probably have the employer reverse the deferrals through the payroll system (which means they will be paid back to the employee now) and treat the money that went into the plan as part of the employer contribution for 2019. There are other options, but this is most likely going to be the easiest (other than amending the plan to make this ok by allowing changes anytime, which is what my plan would have said from the beginning so this issue would not have arisen. FWIW.