Syncing Developer Projects with iCloud Drive

I am a software developer and have been using a macbook pro since the day I started software (more than 10 years). During this time, I also used iCloud Drive and my files were always working in sync. But in the last 2-3 months, I started having problems with the projects. Although the files appear on my device, software programs (intellij idea, visual studio code, xcode, etc.) cannot see these files, or they appear empty when I open them. My programs that work in the evening stop working in the morning. I tried hard to fix it, I logged out of icloud. I logged in again, downloaded all the files again, etc., but if it works fine one day, it crashes again the next day. As a last resort, I considered at least copying my software projects from icloud drive to a non-synced folder on my computer. But now I cannot copy folders from icloud drive. I can copy the files in that folder, but it does not copy another folder within that folder (even if it is empty). First, I need to open that same folder on the target side, then I need to go into that folder and copy the files in it (this way it works without any problems). But as you will appreciate, there are hundreds of folders in software projects and I have 30-40 projects like this. It would take me days to copy all of them one by one in this way.

I'm looking for ways to avoid this sync issue with iCloud Drive in a best-case scenario. If there is no definitive solution to this problem, I am looking for a solution that can at least recover my files from the drive. Apple has never bothered me this much, I've even been thinking about switching to windows for a while (disgrace).