What system are you running on?
I presume by 'keybindings in Python', you mean 'keybindings in IDLE'. Correct?
By 'change to control', do you mean you made a line in the IDLE Preferences dialog, Keys tab, binding box, look like
"keyname - <Control-Key>" instead of "keyname - <Control-Key-X>" ?

The default configuration files are stored in and loaded from pythonxp/Lib/idlelib/. The user configuration files are in <userhome>/.idlerc/. They are not deleted when you delete or install Python. The reason is so that users do not lose their custom configuration when they upgrade or re-install for non-idle reasons. The location of <userhome> depends on the system. On my Win7 system, <userhome> appears as C;/user/Terry. On XP, I believe it was C:/Documents and Settings/Users/Terry/, possibly with 'Application Settings/idle' (or something) added. In any case, delete the bad file, perhaps after uploading config-keys.cfg here with the name 'poisonous_config_keys'.

PS. Usage questions are generally best directed to python-list, where you generally get faster answers. In this case, though, there seems to be a nasty bug. A bad key binding should give a nice error message when one first tries to store it.

Also, try searching the tracker before opening a new issue. Searching for 'key binding' in #11437 Component: IDLE turns up "IDLE crash on startup with typo in config-keys.cfg". So I am closing this as a duplicate. Please post any answers there.