See title. First tested on E6:E, then on a separate instance with only Chisel-MC1.16.5-2.0.1-alpha.4 and CTM-MC1.16.1-1.1.2.6.
Connected textures otherwise work, for instance with CT-Circular and Mosaic tiles for bricks. The connected textures still exist in the files, so I assume it's not intended? Unless there's some config I missed.

Right, pretty easy fix. Just need to add the metadata file for each texture in the textures file of the jar. Looks like there's some other textures missing too.