Atlas files added to resource packs do not get used

The bug

Adding an atlas json file to a resource pack will often have the game ignore it entirely.

How to reproduce

A resource pack is attached to this ticket which adds a new atlas file "block_entities.json", to which several block entity textures are moved.

1. Download and apply the attached resource pack
2. Look at the game output log while this pack is loaded
3. Use F3+S and inspect the files produced in the screenshots folder

Expected results

A message saying block_entities.png-atlas was successfully generated alongside all the other atlases would be present in the output log, and this atlas would be visible in the debug screenshots folder.

Actual results

The output log does not say this, and the atlas is nowhere to be found in the debug folder.