I keep trying to unmap F1 from help and CTRL+M from the toggle menu. I can change the settings, apply them, then go out and come back in and they are back.

I need to pass these keys through KRDC to a remote machine and nothing I have found will pass these keys. Unmapping them and they come right back. Choose Grab Keys in KRDC and it still doesn't grab them.

How can I change this?

I don't know anything about KRDC,if you can run commands on the remote machine, you can use xdotool or xte to simulate keyboard input.
It might not be convenient, but you can bind the command to a keyboard shortcut (on the remote machine, one that is not grabbed by the local kde).

Another thing to try is to find where are the config files for the shortcuts and edit them directly.

Where are you trying to unmap them? They need to be unmapped on a user wide basis - rather than an application wide basis by using System Settings.

The needed settings are located at System Settings > Shortcuts and Gestures > Standard Keyboard Shortcuts.