Does changing Microsoft Users Domain Break Entra or Intune Connection?

I recently moved my domain from a 3rd party provider (GoDaddy) to my Microsoft tenant. This gave users our custom domain name instead of the previous ******@CompanyLLC.onmicrosoft.com type login. Since then, I have had users randomly locked out of their accounts in which I cannot reset the password to allow them back in. Working with Microsoft support, I remade the user's Windows profile and tried to move as much data as I can

Users are also getting the message "Work or school account problem - To fix this, select this notification to sign in again. Or, go to Settings > Accounts > Access work or school settings, and select Sign in again to fix your work or school account" Here they select "Sign in" the box comes up, spins, seems to sign them in, then the notification will show again in a few hours.

I've also noticed that since our LLC account changed to our custom domain, we have three accounts showing here now under the Work and School area. I couldn't add a picture but there is:

-Connected by ******@CompanyLLC.onmicrosoft.com (Connected to Company LLC MDM)

-Connected by ******@customdomain.com (Connected to Company LLC's Entra ID)

-Connected by ******@customdomain.com (Connected to Company LLC's Entra ID)

*The second two are identical and there is no way to tell if they are both to the same tenant or different*

I am trying to get ahead of this issue instead of just waiting for these Windows profiles to randomly stop working mid-day. I ran dsregcmd /status remotely on all of my PCs and I found two different issues.

Almost all users registered their devices with our Microsoft tenant, so they have the right TenantID and have this error:

However, some users seemed to have registered their devices with the GoDaddy tenant and have this error:

Please Note I through so "X"s in the identifier strings because I'm not sure if I'm meant to keep those private.

If you have any solutions for this, I would be extremely grateful!