Just a comment. I don't personally have this issue but did a Factory Restore taking me back to Windows 8.0, then upgraded to 8.0 Pro w/media Center last night. When I upgraded to Windows 8.1 Pro w/media Center Both Window8.1 Pro and Windows 8.1 update were installed together.
Sounds like your Recovery partition was not damaged by installing W8.1, a counterexample to this information:
<quote>
when you upgrade through the Windows store, it wipes out the recovery partition you got with Windows 8, and doesn’t rebuild it with the update
</quote>
So, what set of users falls into that category?