All program activity is paused during deactivation, so any contacts that trigger the event during deactivation are not recognized and do not enter when you reactivate the program.
The program can be deactivated without missing new contacts, but no longer than 1 hour. Work out all program changes before the program is deactivated.
Send times when a scheduled send time passes in a deactivated program
If a program is deactivated during a scheduled send time, all contacts that reached a scheduled email step will be sent at the next scheduled send time after the program is reactivated. Deactivating the program, changing the send time of the email step, or deleting the program does not stop the email from being sent if the contact already reached that step. You can determine whether contacts reached the step by opening your program and clicking Current contact status.