I'm thinking about re-installing windows to make my secondary drive my primary drive, and to carry everything over i would back up all my data on to a external drive. After i made a clean install of windows and transferred all my data back to my internal HDD would 2 copy's of windows being on the same drive affect the transition, or would i just not be able to transfer any of the files in the windows folder back to my internal. Also after the clean installation and transfer of data would windows automatically revert my drives primary/secondary settings back to where they were before the new installation. Please help i cant find anything on the internet about my problem.
Assuming you have mainly Windows/progs on one drive and Data on the other, why not partition the Data drive, and with the Windows drive disconnected, clean install a fresh copy of Windows on the (Formatted) new partition? Then re-connect the old primary drive, set your BIOS to favour the drive with the new install. Then you can do what you like with the old Primary drive, copy data across once Windows removed. You could also consider cloning your Windows installation on to the new partition.