I want to clarify that this is what happened to me. I cloned the internal drive into an external one to have a backup. I installed a different version of MacOS, didn’t like it and went back to the old one by restoring the internal drive with the backup. Everything was working well and fast as usual boot the boot process took a while to display the Apple Logo. It seamed as if the system was having a hard time finding the boot drive. I did what you suggested in this guide and was immediately fixed 😀