Perhaps this is why...
pid 0 (MiNT): arafs: __unlink_cookie: nlink > 0, inode not deleted
pid 0 (MiNT): block_IO : ../block_IO.c, 96796672: Specified cache size too small (0).
pid 1 (xaloader): run_km(\c\MINT\XAAES\xaaes.km) ok (bp 0x6F360E0)!
This suggests its loading xaaes module from the 'C:' drive.. which probably means xfs extensions are not being loaded (in particular ext2.xfs).
So I copied ext2.xfs and rebooted and so re-gained access to all the files on 'd'.
But still for whatever reason I couldn't boot from 'E' despite setting:
'BootDrive = E'
in aranym 'config'