Well what a palaver this was!
When I installed Windows 8 originally I also installed the Desktop app, because it wasn't baked into the OS, and as much as I love Windows 8, I still mainly work in the Desktop - it's where all the hard grafting is still done.
So anyway, roll on a few months and I pluck up the courage to install Office 2013, which comes with SkyDrive Pro, now this threw its own spanners into the work because of the damned upload manager which comes with Office 2013 and it not wanting to work with my personal SkyDrive where I have ~20Gb of Windows admin tools, Android tools and ROM's and other random junk.
Even after removing SkyDrive Pro and installing SkyDrive I had some odd behaviours thanks to the upload manager from Office 2013... and a second copy of SkyDrive folder existing on my computer which accounts for the missing things I thought I uploaded to SkyDrive... so two copies of SkyDrive, one a few months old, one new, I had been using both without realising there were two. One showed in Favourites the other didn't, one I navigated to manually and had a shortcut I used, which pointed to the 'old' one. I hadn't realised this just yet though....
... then came along Windows 8.1 and SkyDrive baked into the OS.
Oh boy, this is when I noticed the new SkyDrive just below favourites and actually took the time to investigate why I was missing files as it seemed to get worse. It got worse because I started using the new SkyDrive folder below favourites, yet when I clicked the other links I had, they were not up to date, I'd check SkyDrive.com and it was up to date... with what I had put in the new SkyDrive shortcut / perma-favourite.
So now I've realised what had gone wrong, I have .old'd the SkyDrive folder, renamed the other which more up to date from SkyDrive (2) to plain old SkyDrive. Now the laborious task of merging them without duplicating files, oh that's right I had also "cleaned up" one of the folders a few days before, so I've got to be careful which way round I do this, because I sure as hell don't want multiple copies of Android ROM's in different locations.
If you've got SkyDrive installed as a Desktop app, DO NOT install Office 2013 with SkyDrive Pro and I'd go as far as saying uninstall SkyDrive, .old the folder, THEN update to Windows 8.1, once you sign in for the first time, move the files into the new SkyDrive folder to ease the bandwidth usage if you're constrained by such things we were concerned about a few years ago.
I don't particularly blame Microsoft for this, but a nice prompt to say "Oh we see you've got SkyDrive installed, do you want to install SkyDrive Pro and the Office 2013 upload manager?"