Based-on Master Pages don't inherit Primary Text Frame
When we create new documents with facing pages and Primary Text Frames on, new master pages are then created based on that original master page.
I would expect them to inherit the same threading and Primary Text Frame designation as the original, but they don't. Only the text frame on the right hand master page is designated as part of the primary text flow, and the frames are no longer threaded. Designers have to check every based-on master, re-designate the primary text flow, and re-thread the frames.
The steps to reproduce are:
1. Create a new document with Facing Pages and Primary Text Frames enabled. The A-Master spread has primary text frames on each page, threaded together.
2. Create a new master that is based on the A-Master. The new master spread only inherits the Primary Text Frame on the right hand page. The page on the left gets a basic text frame, and the frames are not threaded across the spread.
This issue was fixed in the March 2018 (13.1) release of InDesign. Please update your InDesign version to get the fix.
You can also refer to the Release Notes which mentions the fix here: https://helpx.adobe.com/indesign/release-note/indesign-cc-march-2018-13-1-release-notes.html
Adobe InDesign team