Well, I ran across this tidbit that might shed some light on the SkyDrive stuck-in-pending thing. This may not be a pure Windows 8.1 problem like the article implies, however, maybe just a "mass sync" issue, but it does supply an explanation and possible consistency fix:
Couple that tip with the above answers on the MS board to reset the sync by deleting the Skydrive folder (or delete the problem files themselves before trying again), and maybe things will be smoother especially for the larger quantities of files.
One of the most annoying issues with Windows 8.1 is when the newly integrated SkyDrive won't sync files. Often, that's because you have a lot of files trying to sync and your PC is hibernating or going to sleep before it's done. When you turn your PC back on, SkyDrive sync spends so long rebuilding the sync list that it doesn't get through all the files before you're turning off your PC again – with all the new files you created only making the backlog worse.
Open the SkyDrive app and wait a couple of minutes and you should see the total numbers of files that need to upload and download. Tap the numbers to see a list of files with sync progress bars. Create a power profile that doesn't turn your PC off after a set time, switch to that and leave your PC plugged in overnight, and SkyDrive should plough through all the files. If there are files causing problems, they'll be listed here as well, so you can find and fix them.
Couple that tip with the above answers on the MS board to reset the sync by deleting the Skydrive folder (or delete the problem files themselves before trying again), and maybe things will be smoother especially for the larger quantities of files.