Breaking an invisible association between Folio Documents

I created a template InDesign Document (not officially saved as a template, just a document that I do a save as and rename and put new content in.) for my Folio pages. Unfortunately, there is this invisible connection between the new document and the old document to the point that clicking on a text box or a page will sometimes open the document it was copied from. Also, when I am working in a document it is slowed way down. I click on something and I get the color wheel and I noticed in the file window it is saving to the .idlk file and going back and forth to the original document. How can I break this connection?

Working in ID 2014 creating iPad Folios

Thanks