I have two linked accounts and I want to delete one, will I lose my saves on the remaining account if I unlink both?
You should always backup your saves.
But the answer will be "No, you won't lose your saves". Since Nintendo does not allow you to go into settings and delete a user that has a linked account you need to unlink it first.
Example: console has 3 users -
UserA (
linked),
UserB (
linked) and
UserC (
not linked)
1. Go to Linkalho and selected "Unlink all accounts", follow the on-screen instructions and let the console reboot.
2. (UserA, UserB and UserC are now
unlinked but all saves should be preserved)
3. After the console reboots, go to your settings/user accounts and delete the
UserB (or the user that you don't want anymore). Make sure you backed up that user's saves previously if you want them.
4. Only
UserA (
not linked) and
UserC (
not linked) remain
5. Go to Linkalho and selected "Link all accounts", follow the on-screen instructions and let the console reboot.
6. Both
UserA and
UserC are now linked accounts