mac – How to Permanently Remove Old iCloud App Folders from Mobile Documents on macOS?

On my MacBook, when I navigate to the iCloud directory via Terminal with the command:

cd ~/Library/Mobile\ Documents

I see multiple folders related to old iCloud-connected apps that I no longer use or have installed. Most of these folders are empty (0B in size), but they persist in the directory. For example:

ls
27N4MQEA55~pro~writer
3L68KQB4HG~com~readdle~CommonDocuments
57T9237FN3~net~whatsapp~WhatsApp
5U8NS4GX82~com~dayoneapp~dayone
...
iCloud~dk~simonbs~Scriptable
iCloud~fm~overcast~overcast

I’ve attempted to delete them using the following commands:

sudo rm -rf [file/folder_name]

or

find . -type f -size 0 -delete

However, the folders either persist or reappear immediately upon running ls again.

Additionally, when I check System Settings > Apple ID > iCloud > “Show All” (linked apps), these apps do not appear in the list of connected services. Apps such as Pro Writer, Day One, Scriptable, and Overcast, which I have no current association with, still appear in the Mobile Documents folder.

My goal: I want to clean up the Mobile Documents directory to make it easier to navigate and manage files for currently used apps.

Questions:

1. How can I permanently remove these obsolete folders?
2. Is there a way to force a sync reset or clean stale app references from iCloud storage?
3. Could these folders be reappearing due to a macOS or iCloud background process?

Any insights or solutions would be greatly appreciated.