I have never run into the problem you described. I have a dual boot Linux/Win10 (2 drives). Clonezilla image either drive saves the entire disk (bit for bit) so when it gets restored it acts exactly the same. Clonezilla goes on a bootable USB disk, so if you are using Win10 you may need a program called Rufus to write the .iso to the USB drive and make it bootable.
Maybe I didn't describe the issue well enough, or maybe you do have a solution. Let me break it down more precisely, so I can learn what I might be doing wrong then:
****EDIT*** I re-read your comment, and I think I see the disconnect - you said "when it gets restored" - that's my issue - I want to test it before I restore it to my system.
If the clone is bad - I just wiped out my system *AND* I have a bad clone! Now I'm in trouble. I want to test that clone w/o messing up my current running system /****EDIT****
A: I'm booting/running (for example), Xubuntu 18.04, from my internal laptop drive.
B: I use some tool to image/clone Xubuntu 18.04 from my internal laptop drive to an external USB drive. All is good so far.
C:
HERE IS MY ISSUE: How do I now boot that external clone to test it? It has the same UUID as the internal (it is a clone), and IIRC, the boot-loader either gets confused when it sees two drives with the same UUID and locks up or quits, or just picks one or the other outside of my control (I don;t recall which, but it didn't work for me).
The only ways I know of are:
A) remove the internal drive (and maybe also refresh GRUB?) so it sees the external (and then refresh GRUB again to see the internal when I switch back?), or ..
B) Jump through some hoops to change the UUID of the clone (and maybe also refresh GRUB to see the new UUID?), so I can choose either one at boot.
Not the end of the world, with a verify I should be able to have confidence in the clone, and if my internal really did crash, I'd be doing a recovery and there would not be two identical UUIDs to cause any problem, so it should boot just fine. But I really miss the Apple method of clone, reboot with option key, and select any boot-able system it finds. That was easy/convenient.
So how can I boot from my clone w/o removing my internal drive?
-ERD50