Sudden duplicates of volumes (10.13.6)

I'm still running this machine from the 2nd ssd, for which I was able to move over most of my settings. Some of them came flawless, some apps lost settings or serials or had to reinstall. Wacom is notorious. Safari is behaving very slow and in the next few days I will have some dealings with Creative Cloud I reckon.

The primary ssd is still a mess. As soon as the secondary ssd works (more or less) flawless, I have to wipe that ssd and reinstall an older backup. As for now I have to make up for lost time. Still no idea what has caused this as no new software or updates were installed the past few days. Grrrrr.

Thanks for sticking with me BDAqua. Luckily I have both. But somehow I always worry that I'll miss something by going that route more direct. Thanks! Two things though: Safari being slow was due to an older version. Software Update only gave the update half an hour ago. Weird. And Gatekeeper gives me some issues with friendly apps. I ran sudo spctl --master-disable but that doesn't do much for rules already in Gatekeeper. I once saw a thread that dealt with that. Any ideas?

In the meantime I found out some kext are in the quarantine folder and also found a Terminal command to remove them but it's not working. Here's what I found:

 sudo xattr -r -d com.apple.quarantine /path/to/MyApp.app.

and

 sudo xattr -d com.apple.quarantine /path/to/MyApp.app.

Should moving manually work in Safe Mode?

Yes, the home folder. Usually files on the desktop, created by iWork suite or TextEdit.

Yes, I use iCloud Drive.