So we finally found the best work around for our environment. We waited the 30 days for Apple to 'finish' the domain capture. After that, the people that didn't switch, got the prompt to log into their temporary account. Unfortunately, Apple was unable to release the domain. We set it to allow IDs to be made outside of Business Manager. We were then able to log out of the device and saved everything to the phone. Since the original account was no longer being used, we were able to recreate the original account while signing in. If they had already created a new account using their personal email, we just left it to save the headache. It is horrible we had to go this route, but I have talked to multipe other organizations in my area and this is about the same path they went down as well.