That will clear the profile.
And then run the wizard again, to get all the basic stuff.

I'd recommend saving your profile periodically.
File > Save As.
Just so you can revert to whatever previous point worked, if something gets borked.

Also, if you clear the profile, you can start IS Boxer Toolkit twice.
Use one of them to open a saved/older profile.
And the other for the new or cleared profile.
And copy/paste mapped keys across, to not have to redo everything.