This issue should be resolved with patch 0.2.0. If you continue to experience this issue, please reach out to us through our support site to let us know.
Players are reporting that upon deleting a blueprint, remaining blueprints or parts of a built structure may also become deleted.
The majority of cases seem to be caused by players building on top of an unfinished blueprint that is the only point of contact with the ground or base structure. It is recommended that players complete unfinished blueprints to prevent this until a fix or change has been made to the building system.