Entire folder missing from home screen
I had the same issue, and finally figured out a way to fix it!

There are 2 ways to fix this issue, either via iTunes or on the iPhone.  The iTunes route is quicker and if you have a lot of apps in that missing folder you might not remember all of them and iTunes gives you the full list.


Go to iTunes with your iPhone plugged in and click on your phone.
Go to the apps tab
locate all the apps that where in that folder and remove them. 

I actually removed all the apps except 2 that I didn't want to remove just yet because they had data on them that I didn't want to lose. Interestingly enough after removing all the other apps the 2 apps I didn't remove resurfaced on my phone without the folder.  So quite possibly maybe just try to remove 1 or 2 apps from that folder only and see if the other resurface, which makes this process all that quicker and better.
Now reinstall all the apps you removed and they should all reappear back on your phone with out the folder.
Make a new folder and put all the apps back in.  


Voilà, there you have it!