Load BootMii Configuration Editor in HBC, set autoboot to system menu, delay 0
If that does not work you will need to reinstall the system ios and menu. Test wadmanager from HBC, your wiimote will probably loss sync. If it does you'll need a gamecube controller, unless you have preloader installed.
Are you sure you hit backup and not restore by mistake? Anyway, since you have bootmii, this wont be to difficult.
You'll need to install IOS70-64-v6687 [Patched][FreeTheBug].zip first
from wadmanager using ios249
If your wiimotes dont sync use cboot2_wadmanager_1.5_mod.zip