Minecraft Shaders do not convert at all.
This pack is Format 1 Conversion to Format 46 completes with no error but will not load
Looking at the packs before and after , I can see that there is an attempt to do something with shaders and post processing. The removal of these directories allow the pack to load. It will be a while before you are able to get this to work. Mojang changes the rendering code very often
There is not any shader conversion at the moment. It could be that it's trying to use some out of date version of it. Will have to look into it at some point.
I added some shader stuff in my 1.21.4 branch btw, give it a try with that branch but no garuntees