This special-casing ignores that we might have a locked file, so the
hashtable does not represent the contents of the file we want to
write. This causes multivar writes to overwrite entries instead of add
to them when under lock.

There is no need for this as the normal code-path will write to the file
just fine, so simply get rid of it.

When we delete an entry, we also want to refresh the configuration to
catch any changes that happened externally.

This allows us to simplify the logic, as we no longer need to delete
these variables internally. The whole state will be refreshed and the
deleted entries won't be there.