Currently, if Reconcile before build is checked on the Repository, that applies to the repository if referenced in the build and not just on the checkout. This causes a reconcile even if the only repository step is a label step. This can result in built artifacts getting removed before being published. There are two possible fixes
1. A new repository setting which will prevent cause a reconcile if the only reference is a result of a checkout.
2. A repository reconcile step type that would allow a user not to check the box but still perform a reconcile.