Unpublished reference that is not yet prior art

[MR]

During a search, an examiner might discover a material reference that is not yet published (e.g., an earlier-filed application that hasn't yet been published).  Such a reference, if sufficiently close, could, whenever it publishes, potentially render some of the claims of the application being examined invalid. How would the examiner handle such a reference? It seems to me that even if the examiner only searches published references, an unpublished reference could be made of record by a third-party submission.

[lazyexaminer]

A provisional rejection can be made. See MPEP 2136.01.

[MR]

I intended the question to apply to an application filed post-AIA; sorry, I should have mentioned that. 2136.01 appears to apply only to examination of pre-AIA applications.