Windows – How to Delete Old pagefile.sys and hiberfile.sys on Secondary Disk

You could use setacl to replace the orphaned SIDs with a new one. For example, use the following to replace your old SID with the new one:

setacl.exe -on C:\ 
           -ot file 
           -actn trustee -trst "n1:S-old-501;n2:S-new-501;ta:repltrst" 
           -rec cont

Yes it is possible to dual boot both Windows 10 and Ubuntu 16 on separate disks. Often times installing Windows 10 before installing Ubuntu is preferable because Windows is a little picky, but its issues can be resolved.

If you are certain you want to wipe the drive so you can install Windows 10, you may use "Disk Utility" found in Ubuntu or use the Windows Installation further on. In "Disk Utility" select the second hard drive, the one you wish to format and later be for Windows 10, Press Ctrl+F or right click and choose "Format Disk", to bring up a prompt labeled "Format Disk". Now of your choice of "Overwriting existing data with zeros" to make files non-recoverable or "Don't overwrite existing data (Quick)".

Before you installing Windows, you need to remove the primary HD so that Windows will not risk your primary HD. Assuming you know how to create an installation disk/usb for Windows 10, we'll continue with important installation steps for Windows 10. I'd recommend changing the disk partition table to GPT rather than MBR, for ease. Press Shift+F10 after when you choose "Install" for the time. This should open a command prompt. In the command prompt, type diskpart. List the disks available with list disk. The HHD should be listed with a number; select it with select disk 0. If you haven't formatted/wiped the disk run clean. To convert to gpt simply run convert gpt. Then finally, exit and exit again. Continue with installation. When confronted with the partitions allow Windows to do your work.

After you install Windows 10 re-install the primary HD (the SSD). In BIOS after doing so, you may have to change the boot order to the partitions such that the SSD is primary.

You should be able to access your grub; however, Windows may not be showing. So you would likely need to go back to Ubuntu where you would do the following steps (as found on this post in AskUbuntu):

1. Boot Ubuntu and mount your Windows partition (simply open the disk on Nautilus)

2. Run the following on the command line (Ctrl+Alt+T):

   sudo os-prober
   

3. If your Windows installation was found, you can run:

   sudo update-grub
   

Note that step 2 is just for your convenience. You could just mount the Windows 7 partition and then run update-grub.

After that point, Windows in theory should show up in grub whenever you boot your computer, as well as Ubuntu.

I recommend being knowledgeable about partitioning. You do not want to mess up. This little guide was simple and quick, but it is always better to research by yourself before you start doing anything. If anything goes wrong, stop, and start researching the issue so you don't mess up.