By "shortcut" I meant "custom search engine keyword". Like "g" is for google, I have d for a dictionary search. It gets replaced by "duck duck go" every time an update comes along, and now is gone for good...

I strongly support this, I have been deleting the file with every update, as well.
I have a user-defined shortcut on 'd', which gets overridden every time a new update comes along. Now I can't get it back. Please allow us to change the default search engines. I see the security concern in altering the file; hence the hash in the first line. But please consider allowing users to change at least the shortcuts.