Is there a way to see if a SQL 2012 Replication publication is marked for initilazation and a way to unmark it?
Microsoft has some documentation on Initializing and Reinitializing Transactional Replication. 

Initialize a Subscription with a Snapshot

Initialize a Transactional Subscription Without a Snapshot 

Reinitialize Subscriptions

Snapshot Options

From your concern over lost data, you might want to investigate the Snapshot Options. Note this option: Specify an alternate snapshot folder location instead of or in addition to the default snapshot folder location.