One option would be to erase your Time Capsule using AirPort Utility in your Applications > Utilities folder. You'd of course lose your backup history if you did this, but if there are no problems with the device you could simply create a new backup.
The A1302 and A1409 Time Capsules both have very similar designs, so the guides are largely interchangeable. I've swapped hard drives in several model Time Capsules without issue, but I've never attempted it with a drive larger than 3TB. It is possible that larger drives wouldn't be recognized properly, but it wouldn't hurt to try.
The USB port on the Time Capsule is designed for use with a shared printer, but I can't see any reason using it for an external fan would be an issue.
Once you've removed the drive from the Time Capsule, you can still access the data by putting it into an external enclosure, though the backups are stored in password-protected disk image files that you'll need to mount.