When trying to create a new QC project based on a template (or trying to "save as" with "Make a copy of the layers") not all feature layers are copied to the new folder. There is no indication it happens or why it happens to the same layers every time. When checking the new QC project it links back to the template feature layers rather than the theoretical new ones.
Please email quickcapture.esri.com to arrange a call to troubleshoot this.