Boot time has drastically increased after restoring partition

I have made a backup of my Linux Mint Xfce partition and I have restored it (all with "Disks" - gnome-disks) twice. (More here ). The partition includes all the system (no separate partitions between /, /home/, /boot etc, just /.) After each restoration the system works fine, but the boot time is very long (2-3 minutes) compared to what it used to be (20 seconds maximum). Why is that and can I fix it? As I shut down every day I am thinking about reinstalling my system but I would prefer to avoid that, as it would be what the whole backup process was trying to avoid. --- Update: I have found a similar situation when shrinking a system partition with a similar system. The situation improved when the same partition was increased back to its initial size. Possibly the system is looking for a "familiar" size of the partition at boot-up and asks for more boot time when it encounters a smaller size...