Windows 10: How to delete "Boot" folder from my old drive

I am using windows 8.1 and renew my windows many time with connected hard drives of 4 TB and 2TB with very useful and personal data.How can I delete this folder without formatting my whole drive.When I install windows it boot up but with drive connected it says error to boot and make need to boot from bios manually. It makes confusion in boot of my current OS.Please help me if someone knowns how to delete these folders.When I install windows it show these partition as system. How can I convert these partitions from system to primary without formatting.

:)

 

Trouble deleting a folder

Thanks for the suggestion but it says "delete folder failed for E:\....." for each folder I try.

*Confused

Will I be forever stuck with these unnecessary folders? *Oh Well hwell:

 

Unable to delete a folder - Invalid folder name


Suggestion:

1. Run chkdsk x: /r to make sure that there's no HD corruption.
   x: is the drive containing the folder you want to delete.
2. Try to delete the folder again. If still does not work, go to step 3.
3. Download: Download - Linux Mint and create a bootable USB using: Rufus - Create bootable USB
4. Boot up with Linux Mint and try to delete the folder again.
   NOTE: Unlike WinPE. Linux does not have any Windows permission imposed to it so it is easier to delete.

 

Deleting the WindowsApps folder on secondary drive?

Hmm, which is faster. I attempted a Live Linux Drive already but it was very slow and would not boot, not to mention I don't know a thing about using linux.

Would option 2 be easier? I looked at Macrium, but the install steps themselves are confusing me, and I fear not knowing how to navigate it once I boot to it.

EDIT: I installed Macrium Reflect Free, went through these steps to create the media.
Don't forget to check the UEFI/MBR box if you are attempting this yourself.
I then booted to it, "browsed my files for an image", but for real, navigate to the WindowsApps folder on your secondary drive, and delete it. It doesn't disappear instantly, but when you exit the drive, and log back into windows, the folder will be gone.

Thanks for the suggestion cereberus!