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. After this small window, all program activity is paused during deactivation. Contacts that trigger the event during deactivation won't enter when you reactivate the program.
Send times when a scheduled send time passes in a deactivated program
If the contact already reached a particular step, deactivating the program, changing the send time of the email step, or deleting the program doesn't stop the email from being sent. If you deactivate a program during a scheduled send time, all contacts that haven't reached a scheduled email step will be sent at the next scheduled send time after reactivation. You can determine whether contacts reached the step by opening your program and clicking Current contact status.