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The old installation would have been on MBR partitions - for new Windows 10 installations now you need to be using GPT partitions to support the install in UEFI Mode now.
Somewhere in the clean install it will show you the existing partitions, Optionally at this point you can select to delete them and re-create them - Windows will create the new style partitions then to keep Win10 happy.
this screen
Keeping in mind you are going to loose all software and files created previously at this point.
I've had a similar problem to this in the past, the installation might be getting confused with the second hard drive you have connected.
If you get into the box and disconnect that temporarily and try again it should work ...