Don’t get me wrong, Wii U Account Swap is a useful homebrew program and I do use it myself. However, I can only recommend it for advanced users because, as you’ve noticed, it is possible to accidentally lose your account data if you use it wrong. If you unlinked your NNID before backing up the account.dat, your NNID data is lost now, unfortunately.
Check the usage section of the readme on GitHub for detailed instructions on using it. There is a specific order you need to follow to ensure all your account data is stored safely: backup NNID => unlink NNID => sign in to PNID => backup PNID. Then, after that initial setup, you can use it to swap online accounts.
In your specific situation, it might be possible to backup your PNID => unlink the PNID => disable Inkay => sign in with your NNID => back up your NNID. I’m not certain whether this will work but it’s worth a try.