I've made a folder which contains Python projects and entered it into Windows Defender's exclusion list, but every time I make a new project in PyCharm I'm being asked to exclude the folder inside the excluded folder. Is there a step I'm missing?
I've added the whole parent folder into the exclusion list and opened new project folders inside it.
You are not missing any step. If a directory is excluded, all of its descendants are also excluded.
This is a known problem with PyCharm. Disable that notification and move on.