To change the shortcut of a service, run plutil -convert xml1 ~/Library/Preferences/pbs.plist
, open the plist, and change for example
<key>(null) - Some Service - runWorkflowAsService</key>
<dict>
<key>key_equivalent</key>
<string>@~a</string>
</dict>
to
<key>(null) - Some Service - runWorkflowAsService</key>
<dict>
<key>key_equivalent</key>
<string>@~</string>
</dict>
Then restart to apply the changes.
@ is command, ~ is option, and  is delete (Windows backspace). Forward delete (Windows delete) would be . The shortcut strings use the same format as in DefaultKeyBinding.dict.
To change a global shortcut set in the App Shortcuts section, run plutil -convert xml1 ~/Library/Preferences/.GlobalPreferences.plist
, open the plist, and change for example
<key>Some Menu Name</key>
<string>~@a</string>
to
<key>Some Menu Name</key>
<string>~@</string>
Then quit and reopen applications to apply the changes.
Application-specific shortcuts are stored in ~/Library/Preferences/*.plist and ~/Library/Containers/*/Data/Library/Preferences/*.plist.