The instructions that I posted in this discussion long ago are not suitable for OS X 10.11 ("El Capitan") or later. If you're running El Capitan, followed those instructions, and now can't empty the Trash, please take either Step 1 or Step 2 below (not both.)
Step 1
Restore from the backup you made before moving the folder to the Trash. If you backed up with Time Machine, follow these instructions.
Step 2
This procedure will temporarily disable System Integrity Protection, a security feature of OS X that is preventing the Trash from being emptied. After you empty the Trash, the feature will be re-enabled. Nothing else will be changed.
Start up in Recovery mode. In the OS X Utilities screen, select Get Help Online. A copy of Safari will launch. While in Recovery, you'll have no access to your history or bookmarks, but you won't need them. Load this web page.
Triple-click anywhere in the line below to select it:
csrutil disable
Copy the selected text to the Clipboard by pressing the key combination command-C.
Quit Safari. You'll be returned to the OS X Utilities screen.
Select
Utilities ▹ Terminal
from the menu bar. A Terminal window will open. Paste into the window by pressing the key combination command-V.
Wait for a new line ending in a hash sign (#) to appear below what you entered. If it doesn't appear, press return.
Quit Terminal to return to the main screen.
Restart as usual. You should now be able to empty the Trash. As soon as you've done that, start up in Recovery mode again and load this page in Safari. Run the following command in Terminal as before:
csrutil enable
Restart as usual again.