Problems with storage and icloud

I have a M1 pro 2021 macbook 14 inch. Recently, I ran a large number of simulations of OpenFOAM, which is a fluid dynamics simulator. This creates a massive number of new folders and directories and files. I'm not sure exactly what happened, but my entire file system is now slow, even though I still have plenty of storage left. Random code files are just deleted which is incredibly frustrating, because I've lost weeks worth of work. All my files have the cloud with arrow symbol next to it, so it seems that none of my files are actually on my computer. I want to have all my files locally, but also backed up to icloud. And I don't want this to happen again when I run another set of simulations. Also, at the bottom of finder when I am in the icloud tab, I am seeing a message like "uploading 700 items, (11 gb out of 130gb). Why is this happening??? It's been trying to upload for the last week. I'm at my wits end

[Edited by Moderator]