I just wanted to make a thread in case this happens to anybody and they run across this in a Google search.
 
I am using an EVGA CLC 280mm AIO cooler and have noticed that when Flow Control is running, I cannot use either delete key on my Microsoft Surface Ergonomic Keyboard that is connected via Bluetooth. The delete keys register with EK Switch Hitter, which shows that it's a software problem and not a hardware problem. Closing Flow Control will allow you to use the delete key again.
 
The workaround is to apply your cooler settings in Flow Control and then close the program. The settings will be saved to the firmware on the cooler and it is not necessary to run Flow Control to use your custom settings.
 
Edit:  I made a video of the problem and posted it on YouTube.  This forum's software seems to edit out YouTube links but you can find it by searching for "EVGA Flow Control Disables Delete Key in Windows 10" on YouTube.
 
Environment:
Windows 10 Pro x64 v1607
EVGA Flow Control 2.0.0.3
Microsoft Surface Ergonomic Keyboard
Asus BT-400 Bluetooth 4.0 USB Dongle