Thanks for the help bigfoot. As it happens a friend suggested the same thing. You're dead on.
When adding the new drive I must have synced some files before it was properly mounted. That's confusing as hell. I didn't know you could mount a dir on a non empty dir. Many hours lost troubleshooting that one. Hopefully someone finds this and avoids the same rigmarole.
The upside is I'm well versed in Amahi, Greyhole and Linux basics now
Here are my steps should they help:
Root drive is full, Amahi crashes. SSHing to box and running 'df -h' shows only significant files in /var/hda/files/drives - the mount location of your external data drives.
Even though you are mounting external drives at /var/hda/files/drives over a folder in this location, there could still be files in the underlying file system. In my case from a Greyhole sync when a new external drive wasn't properly mounted. With the data drives mounted it's difficult to tell what's underneath.
- Disable Greyhole
- Add 'nofail' as an argument to fstab for external data drives so Fedora doesn't hang on boot without them
- Shut down the server and disconnect data drives and reboot
- If there is still data accessible in /var/hda/files/drives then you likely have have your cause for why your boot is full (you could also simply unmount the external drives but I wanted to know for sure)
- Log in to Amahi web UI and create a new (non Greyhole) share e.g. 'temprecovery'
- Move the data out of the boot drive and on to your temp share over SSH e.g. mv /var/hda/files/drives/your_disk/gh /var/hda/files/temprecovery/gh
- On the network, back up your files, then delete them from the share. You can check later if you need them, but it's always best to have a backup.
- On the Amahi web UI: Check out your recovered space under Disk->Partition. Delete the temp share you created.
- Turn off the server, reconnect your drives, turn on it on again, enable Greyhole and profit.
- You will want to edit the 'nofail' argument back out of fstab because if for some reason a data drive doesn't mount at boot in the future, you don't want to risk files being sent to your internal drive again. So it's probably best for the boot to fail if a data drive doesn't come online.