Then it should work - but it looks like you'll have to bite the bullet and let it create a completely new backup. This is from the Setup Guide for your AirPort:
"Using Time Machine with Your AirPort Extreme
If you connect a USB hard disk to your AirPort Extreme, you can use the Time Machine application to back up all your Mac computers, including your photos, music, movies, and documents.
After you set up Time Machine, it automatically backs up your computer on a regular basis.
Use Time Machine preferences to set up automatic backups, use a different backup disk, or adjust other settings.
To set up or adjust Time Machine on a computer using Mac OS X v10.5.7 or later: 1 Choose Apple > System Preferences, and then click Time Machine.
2 Slide the switch to ON.
3 Click Select Disk.
4 Choose your AirPort Extreme and click Use Disk.
Important: Your first backup with Time Machine could take overnight or longer, depending on how much data youre backing up. To speed up the initial backup, connect your AirPort Extreme to your computer using Ethernet. In each subsequent backup, Time Machine backs up only files that have changed since the previous backup, so the backups dont take as long.
If you shut down your Mac or put it to sleep during a backup, Time Machine stops the backup and then continues where it left off after your Mac starts up again.
For more information about Time Machine, choose Help > Help Center from the Finder on Mac, and then enter Time Machine in the search field."
http://manuals.info.apple.com/MANUALS/1000/MA1644/en_US/airport_extreme_80211ac_setup.pdf (Page 13)
I would do as it suggests, and let it back up over night.