I have pinned down the cause of this bug. When ProveIt scans the wikitext to construct the reference list, it creates a Reference object for each reference, so when one of these references is being edited and the user changes the main template, the reference data is still in the background and the reference form can be regenerated with that data. But when a user is creating a new reference, there is no Reference object in the background yet, so when the user changes the main template, the form is regenerated and there is no Reference object from where to fill it. The solution would be creating a Reference object for the new references too.