This is the issue that has been haunting since day 1. Root and mounted files randomly disappears, and only an reboot can fix it.
The issue is that Zygote requires some time to isolate the mount namespace for the children it forks (read: most processes), so in rare cases such as the CPU is on heavy load, or CPU is in deep sleep, it takes longer than usual to finish the mount namespace isolation. Magisk Hide kicks in before the isolation is done, and it will switch to Zygote's namespace and do the unmounting. All children will then lose the mounted files, which includes root.
The solution is to first find the namespace id of Zygote, and wait a small period of time and retry if the namespace isn't isolated yet.
Right now there are three threads (process)
1. Main thread in parent: monitor logcat
2. Second thread in parent: monitor hidelist
3. Children: switch namespace and unmounts
