well, if all of your saves are okay i guess there is no problem formating
to keep my saves safe without having to use saviin and stuff here what I do: when i have games in HDD from time to time i copy them on internal, then i delete everything except the save, so i have all saves on internal, then i copy them on a wiiU formated USB stick, so basically my saves are on: hdd, internal, usb, so if the HDD die at worst i have just to reinstall stuff, and if my WiiU die i can still recover the saves easily like you did on the USB stick
I usually just play one game at once, so when i stop playing it for another game i backup the save like that