Problem with Media Encoder Watch Folders using a AE Project with folders

Hi! I'm starting to test the Watch Folders functionality with Media Encoder because we want to set up sort of a render farm. The idea is to define several Watch Folders for the Designer teams that are shared across the network.

The problem is that when I drop an AEP to a Watch Folder where the compositions are nested in folders inside the project (and this is a necessity), Media Encoder doesn't recognize any composition at all. The render queue in Media Encoder remains empty.

I already tested to place compositions outside the folders in the Project and those are rendered.

Is there any way to "tell" Media Encoder to search compositions in the project's folders/subfolders?

Thanks!