Fix bug caused by synching a repo multiple times in init

If a repository is added multiple times during the sync and a prefix is selected, has_repo will return False for that repository, as it has not yet been added to the prefix, but it has been synchronized and added to repos.cfg, meaning add_repo returns None and we try to sync None.

Since the prefix repositories need to be re-calculated after new ones are added, it makes the most sense to just clear the prefix during sync, and set it again afterwards (updating the prefix's repo list).