Be sure that you don't waste your time by downloading the simple 10.11.4 update, which requires 10.11.3 to work.
Download the 10.11.4 Combo update
I can also point out that I quickly got into some issues with the 10.11.4 system (a personal problem with some of the system "tweaks" that I use), and tried the combo update to fix it, with only partial fix. I then simply booted to my 10.11 4 full install on a flash drive. Ran an OS X reinstall, and took about 20 minutes to complete. I was back up and running normally again...
Reinstall from flash drive:
Download the El Cap installer from the App Store.
Do NOT let the installer run, just quit the installer when the download finishes.
Create a bootable installer, either by using the simple terminal commands - or use the good DiskMakerX app that will do that both easily and even a nice icon on your flash drive when that is done.
Boot to that USB installer. You will see basically the same choices that you get when you boot to the recovery system, but you won't have to wait for all the OS X files to download (they are all on the flash drive.)
"Reinstall OS X is just what it says - a reinstall of the system. You don't lose any of YOUR files and Apps, and it will look just the same as before (should fix your icons, however, which is what you want)
You CAN use that bootable flash drive for a clean install (wipe the drive, then install a completely fresh OS X system), but you would know that you are doing that, because you would choose to erase the internal drive first.
But, you don't need to do THAT erase first, just run the Reinstall OS X. It can take some time (anywhere from 20 minutes to more than an hour), so be patient.
Well I think I found a simpler way. Use an app called LightIcon. It will restore folder icons to their original state or to any icon you create yourself. It takes 20 seconds. I don't know how it does it but it worked. Thanks Freemacsoft!