Steps to reproduce:

1. Create 2 threaded text frames on a page.
2. Fill them with text (Lorem ipsum)
3. Autonumber the paragraphs with Autonumbering feature in InDesign - regular 1, 2, 3-list will do.
4. Create a new layer
5. Move the first frame in the text flow to that layer
6. Turn off visibility of that layer....

The autonumbering is gone from any autonumbered list!!!