No folder hierarchy in Intermediate directory leads to naming conflicts

I am using Unreal to connect a messaging framework by auto-generating publishers and subscribers for it. We use many protobuf messages in a folder structure. If two of those files have the same name, it leads to linker errors and missing object files.

From a look into the Intermedia folder it looks like the folder hiearchy gets ignored for the .obj filenames and they are put into the root of the Plugin/Intermediate dir resulting in that conflict. Why?? Whats the design decision of that? Too long folder names or something?

Is this going to be fixed? I feel like all issues I am facing around integrating into Unreal are with UBT and UHT akward behaviours which is hindering using it professionally!

Bump! Does anyone have a solution to work around this behaviour?

I’m surprised you’re getting to the OBJ file conflict, for me it errors out before the OBJ files are even generated due to header file conflicts because UHT also squashes any subdirectories that would otherwise distinguish between filenames.