TL;DR: merged paths invert when converted to 3D layer after updating After Effects.
I just updated to After Effects CC 15.1.1 (Build 12) and discovered a frustrating change in a project created in a (recent) previous version--I cannot say exactly which version of AE I was using to originally create the project, but it was CC 2018 flavoured.
The project contains many (many) paths which were originally Adobe Illustrator compound paths. I converted these paths to shape layers by importing an AI file and using "Create Shapes from Vector Layer". The resulting shape layers have many paths and AE intelligently added a "Merge Paths" set to "Merge" where appropriate. Originally, I achieved the desired result: complex 3D shapes with the correct portions "knocked-out". One example is a house with windows and a door rendering as transparent "holes" in the house path.
I did not use any 3rd party plug-ins when creating this project and I am interested in alternative work-flows but I also want to solve my problem to avoid re-doing a bunch of work.
My problem: after updating AE to latest, all the merged paths render out incorrectly inverted, e.g. the house is an empty house silhouette with windows and door appearing as solid 3D extruded objects. I can easily re-create the problem, post-update any merged set of paths in any shape layer render correctly (house has transparent windows and door)... until I convert the layer to 3D... suddenly the paths all invert!
I hope I've explained this well enough. Thanks for reading,