Sorry to necro the old post, but I was trying to add multiple modules and thought that adding them via Visual Studio then cleaning/rebuilding/regenerating project files etc… would do the trick, but it wasn’t working… Every time I added a folder/file to my module via Visual Studio, after generating the files, the files disappeared and were marked as hidden files. I tried to reinclude them to the project, and when I did they were placed at the project Source/ level. So I recreated the hierarchy and washed/rinsed/repeated just to be slapped in the face again…
Finally what solved it was creating the files/folders via the Windows file explorer, then after generating the project files they did not disappear and UBT was able to find them and all is working fine now. Thought creating the folders files via VS would be writing that structure to the file system, but it turns out that it strangely doesn’t work like that… Anyhow, hopefully somebody finds this useful