Most likely, yup. If you have titles obtained through the eShop, and then switch to Pretendo, you'll lose access to them. You can delete those, then reinstall them with something like FBI, and they will no longer be tied to an NNID.
I thought that. But I asked bc I thought luma just bypass these eshop-nnid signs. Maybe not with these xD
Nah, the only thing it bypasses are the signature checks. Each title has a ticket, though, and these tickets are unique to an NNID when obtained through the eShop. They sort of act like proof of ownership. When installing through alternative means, a fake ticket is instead installed, and it isn't linked to an account.
That's your issue unfortunately. We don't recommend deleting your NNID at all (I happen to be staff for Pretendo), since you lose access to games you've brought off the eShop.
