We woke up one morning to learn our Win10 ASUS Transformer Book was in the throes of the Win10AE (Anniversary Edition) "upgrade." It works OK, but we were camping and the process kept us from using the PC for a couple hours. AND it devoured our 6gB mobile data allowance...
But, all software applications we had, still work.
I gOOgled how to force my Laptop, a Win10 Acer, to upgrade to AE while I was at home and had 1tB to work with. I was able to do that, and again, all the programs work.
I HAVE had issues with things like touchpad drivers and had to go get new ones. So by extension, you might have to re-install the DRIVER(s) for some of your peripherals. Or do a complete peripheral INSTALL