All you would need to do is re-run Permission Wizard and select top level domain under Users and then re-run Message Store Configuration Wizard and point it also to the top level domain. It should be straight forward. Users should not be affected as long as there is no duplicate alias (Which by default should not be there)
These are the paths to get to each CCX logs through CLI. They may be helpful if you are having issues accessing RTMT or downloading logs through it.
If you want to download them you have to prefix "file get " and you can add one of the options (re...