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How should I format my source disk after cloning?

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So I've got my target disk cloned and am currently able to boot up from it. I'd like to introduce what I had before (my source disk) as a disk for extra space, but I do not know how to format it without it freaking out my boot sequence.

I spent a very long time trying to boot into windows because I had tried booting to windows with both disks in the system at the same time causing a loop of errors. I'm wondering if I can format the source disk in the windows command prompt and then still be able to boot up to windows on my target disk afterwards. 

I obviously want to be very careful because if I start my pc with both disks I don't want it to mess up my target disk especially if it messes it up before I start formatting the source disk. Because at that point I'd have no good booting options!

So I'm asking if anyone has any good ideas for how to format the source disk without potentially causing damage to my target disk because of having both of them in there during the boot up. 

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James, welcome to these public User Forums.

The safest method of preparing your original source drive for use as a second data drive is to connect it via a USB adapter or dock which can be done after you are booted from the new boot drive.  Once the drive is connected, you can then use any Partition manager programs to reformat it and remove the hidden / system partitions that are present on a Windows boot drive.

Note: Windows Disk Management won't normally let you remove hidden / system partitions so download a copy of the free MiniTool Partition Wizard software and use this to do this.