Downloading them screwes up the files. I want to disable that. I want to light it on fire. I've spent decades organizing things to be exactly where I want them. I log in one day and find every cloud service has taken to stealing my work and telling me it's on me to do the unpaid labor of trying to put it back, also pay for more space.
You will have to analyze your workflow and your computer setup.
It's not clear exactly what you are downloading from exactly where. Not one of those Cloud services grab your files and save them only in the Cloud.
They work in a way that there is a synchronizing folder on your harddisk and when you save a file into it, then it gets synchronized in the Cloud. But the copy stays on your computer. If you delete the file from your computer, it will be deleted in the cloud as well. So what you are describing there, can not happen.
You might want to get a computer specialist set up your computer for you.