It's going to be hard to find out what what the problem is unless you can lay your hands on another board or CPU to test.
Have you tried clearing CMOS?
You could take the CPU out to inspect it and the socket for any damage.
Unfortunately, I don't have anyone with the x99 . I checked the processor looks like new xD. Yes. I licked the whole motherboard with battery replacement also
MY Gigabyte board did the same, I suspected the BIOS chips and replaced them but it didn't help. Checking voltages revealed 0v on VCORE so I suspect either voltage regulator/mosfet or a broken track. Impossible (for me) to trace it any further without schematic or circuit diagram. Nothing visibly amiss on the board.
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