Symptoms

Appit takes over SharePoint core functionality, I create a list template from an appified list and instantiate a copy list in SharePoint from that template.
Problems:

1. The new 'Copy' list comes up already appified.
2. Creating a new list item in the 'Copy' list actually creates a list item in the list that the list template was based upon. In other words, the new 'Copy' list stores data in the other list.

 

Diagnoses

This is expected behavior and is by design.
We generally don't recommend creating List templates from an appified SP List. Reason being when you appify a SharePoint List we hook into the list content type to connect K2 pages (New, display, Edit) forms. Creating a template of a List has the option to delete contents but no option to use the content type meaning the list template will have the K2 pages wired to the content.
 

Resolution

Edit the new List created from the template in SharePoint Designer, browse to the Content Type and in the content type you'll see the K2 pages association, delete them and the New, Edit and Display forms will be the default. See video for reference: http://screencast.com/t/kWrafgWfazcr
Essentially, the Display, Edit, and New Form URLs will have the SmartForms URL of the source appified List set the respective URLs as blank by removing the associated SmartForms URLs.

We've logged a request with the documentation team to have this information published on help.k2.com.