According to what is said in the question, the deletion of the directory that was deleted years make that the files contained by it become "orphaned files".
When you "remove" them from your Drive they will be sent to your Trash. From there you could permanently deleted. While the file is on the Trash collaborators might find it but they ...
Inspired by Hamza Safdar's answer, I created an end-to-end Colab for those who are not familiar with Python and Colab at here.
In case people can not access the Colab above, I also add the code as follows:
#@title Deeply copy shared folders in Google Drive
from google.colab import drive
print('Mounting Google Drive...')