Once you save a value to the profile, it remains there until it's explicitly removed. It is an independent piece of data, so whether there is a variable with the same identifier, or references to such a variable, does not affect it.
Deleting a value saved to the profile should be possible by setting the value of a variable with the same name and datatype to "Not set" (I.E. clearing its value, so there is no value), and using the "Save value to profile" option.
Otherwise, all values of one or more given types can be deleted using the "Clear Saved Values from Profile" action.
Note that values saved to the profile database are not exported with a profile.