Can't clone my HDD because of "check file system"

[Jakers038]

I got Minitool partition wizard to clone my HDD (OS and another partition) to a new SSD I got, I started the process, it prompted for a restart, since C was in active use and was going fine for a few seconds until it said something about checking the file system and stopped the cloning. I have been getting the check file system on boot up for a few days now, but always skipped it. Today, after the cloning failure, I let it finish, it said "fixing C stage 1/Stage 2/ 100% complete" and things like that, I restarted again and....again "press any button to skip disk checking", so basically I lost half an hour for nothing just to get the same thing again.

 

I ran the read-only (non-fix) check file system for both C and D partitions inside Minitool wizard, D had no issues, but C had several "orphaned" segments, whatever that means.

 

So what am I supposed to do? I read that some third party programs could make this problem, but I install pretty much everything on other partitions, but still I guess I could try and find every single thing I don't need on C and delete it, but I don't know if that would do anything.

 

I have a lot of interconnected things between other partitions, game document files, program files,etc, so I don't want to install a new windows on the SSD just to spend days on restoring everything that I can, if I could just somehow stop the check disk thing during cloning, it would make life a million times easier.

[Tan3l6]

Are both drives internal? 

[Jakers038]

Yes, I also have a 1TB HDD for games, I only got the SSD yesterday, so it is not related to it, since I have the disk checking thing for over a week now.