Hello @AndrewNelson2
Thank you for contacting the Canvas Community. We're sorry to hear you've been experiencing issues with late policies. So, you can have the x percent period if it's late by actually using the missing policy. You set how much you want to reduce the points/percentage by and then as soon as the due date hits, students that haven't submitted are "late" or missing and they are marked down. There is not a way to use the "late" policy option in the gradebook without the percentage and time in effect, though if you had it over hitting a bottom maximum score of 0 over a day, it shouldn't take that long.
Here is the Canvas guide:
https://community.canvaslms.com/t5/Instructor-Guide/How-do-I-apply-a-Missing-Submission-policy-in-th...
As for the nightly sync change, you need to speak with your CSM or just contact support and inform the SIS team of the change.
https://community.canvaslms.com/t5/Canvas-Basics-Guide/How-do-I-contact-Canvas-Support/ta-p/389767