Sorry for the delay. Thank you all for your replies. So for whatever reason, the issue hasn't happened for about a few days, which is something of a new record compared to the past month. I haven't uninstalled anything, nor changed any settings. As soon as it happens again, I'll try and see what Procmon says.
Do you have carbonite installed by chance?
No, I don't.
any startup services or programs and look a bit off? you should scan with a proper antivirus, defender won't cut it. also any chance the files are being hidden
are they going into the recycle bin? (if so try turning on "delete confirmation" in the recycle bin)
Files aren't going into the recycle and they aren't hidden.
Do you have SkyDrive turned on? If so, go look on the web version and see if your missing files are there. I experienced wonkiness with the Documents folder and saving from certain apps so I turned it off for now.
EDIT: I missed that you mentioned SkyDrive. I will clarify I had to completely turn the integration off not just the document syncing. I removed all my synced stuff and Win 8 device profiles from my MS account and everything seemed to behave after that. I just left the "Save documents to SkyDrive by default" switch off.
I've left the Save to SkyDrive on at this point.
Get Process Monitor from SysInternals. Put a file in your Documents folder, and set a filter in ProcMon to monitor it (and only it--otherwise you'll get inundated with irrelevant data).
When the file gets deleted, you should be able to see what process deleted it.
I will try this.