Yes, doing that method you describe (I have done it myself) will leave your source environment fully operational and without issue. Any subscriptions you have in the source environment won't fully copy over unless you also copy the Agent Jobs from source to target though. .... although that may be what you want.
And if you are going to a different ...
You need to add and extra ) to the end of the first then
here is a sample of it:
when (b.ModuleType in (20) and rtrim(substring(a.PrdAcctId,1,8))='RD')
Are you sure that User isn't part of an Active Directory Group that's already mapped to those databases, for example the default Domain Users group? Users inherit the SQL Server permissions of the Active Directory Groups they belong to as well.
Also if you could elaborate on what exactly they have access to in the database, that would be helpful. Anyone who ...