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To clone or not to clone. That is the question.

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My current computer has two drives - an SSD boot drive and then a regular hard drive for the rest.  I'm trying to replace the 2nd drive with a larger (5TB) drive.  I don't seem to be able to get his to work.  I've posted my drive configuration here: https://gyazo.com/57af59770bd5cbab2b6478e927fac99f

If i copy everything from D to F and then take out D, the system tells me i need to put in the proper boot media.  If I clone D to F and remove D, I get the same result. 

I've also tried backing up D and restoring to F.  Same result.

Any idea how to do this?

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Make sure the computer can boot with only the system disk in the computer. If not, repair Windows "repair the startup of the computer"

THen reconnect the other disks. A disk copy should work, no need to clone or backup and restore.

I suspect that the boot records of the system disk are tracking some boot device on the other D: disk, so when this disk is removed, the boot manager cannot proceed.

I concur with Pat, looks to me like your boot record is on your D drive and without that drive attached the machine will not boot.  A BCD rebuild on C drive is probably going to be necessary.