I have the cloud save with nintendo and am running into the same exact issue if this helps anyone. So it probably isn't that. I saw earlier it may have something to do with the web authentication button on the switch account not working properly so it was removed recently in a hot fix not long ago. ? Not sure. I was thinking that maybe it could have something to do with the email that is associated with my switch account is the same as my warframe pc account. Perhaps there is an issue with distinguishing them from one another if they are the same? I don't know tbh just throwing ideas out.