Found the fix. Open Windows Update and down at the bottom you should see "Get updates for other Microsoft products" with a blue clickable "Find out more". Click the find out more link and IE should open to the Microsoft Update website. Now all you have to do is check the I agree box and click the install button. That should put the "Microsoft Update" option back in and the "Give me updates for Microsoft products..." check box should be checked too.
My Computer
Computer type
PC/Desktop
Computer Manufacturer/Model Number
Home Built
OS
Windows 10 Education 64 bit
CPU
AMD Phenom II X4 980 Black Edition Deneb 3.7GHz
Motherboard
Asus M4N68T-M V2 µATX Motherboard
Memory
8GB 4GBx2 Kingston PC10600 DDR3 1333 Memory
Graphics Card(s)
Zotac NVIDIA Geforce GT640 2 Gig DDR3 PCIe
Sound Card
VIA VT1708s High Definition Audio 8-channel Onboard