It's earlier than I'd said I would report this but for reasons I'm choosing to wrap up this experiment.

In day-to-day usage, I still haven't ran into any problems. Granted I did not play any games on the laptop, but I did run 3DMark after the cloning. However supposedly people do have issues regardless if they game or not. I also may not have been exactly representative of the use case, since I didn't clone after say a year of use. Though I can't think of anything that would cause issues since the only thing that should grow barring the installation of other programs is the Users folder and possibly ProgramData.

There was one other problem I forgot to mention in my last entry since it slipped my mind: the hard drive was offline when I first booted into the SSD. This means Windows knows the drive existed, but it didn't mount it. i.e., it wasn't accessible. I found an article explaining why this was though: http://www.multibooters.com/tutorials/resolve-a-disk-signature-collision.html. Windows has what is called disk signatures, which originally was meant to help the OS configure a software RAID setup. The disk signatures are supposed to be unique, but sometimes cloning software will copy this over. When that happens, Windows will take the other drive(s) with the same signature offline. You can put them back online, however, Windows will reassign a new signature to that drive. However, this is only a problem for that disk. So if you planned on booting into it again, you'll have issues.

The article claims that cloning tools used to either give you a choice in the matter of keeping or assigning new disk signatures. But now they automatically assign new signatures and change the configurations so Windows doesn't freak out.

So yes, there is some grain of truth that if you clone, Windows will run into issues because it's expecting one set of disk signatures and you've changed them. However, this appears to be a combination of the cloning tool and what the user did. Like for example in my case, since Samsung's cloning tool copied the hard drive basically verbatim, if I accessed the SSD right after cloning the hard drive (which is very likely if the person wants to do a soft verification of the clone), it would've changed the disk signature and I would've had issues. But since I booted into the SSD instead, I changed nothing. I'd imagine since few people know about disk signatures and if this was the root cause of their problems, this is why they think the act of cloning itself causes issues.

I used to clone via creating a bootloader partition, cloning C:\ onto the new drive with Partition Wizard (or Magic, I forget which), then making a bootloader on the drive. So disk signatures weren't really an issue for me with this method. However this hasn't been working for some reason or another and I don't really have a reason to clone drives these days so I never figured out why.

My conclusions on the matter:

• Cloning is more or less a safe thing to do.
• You should use the tool from manufacturer of the drive you're cloning tool if they have one.
• If the manufacturer does not have a tool, get a program that is advertised to do so like Macrium Reflect or Arconis True Image.
• After cloning do not try to access the drive. Do a verification by booting into it.
• If you do not see the original drive after booting into the new one, do not try to access it until you're satisfied with the cloned drive.