Since I resolved this issue, I would like to write a solution for everyone who may encounter similar issue in the future.
What you will need:
1. A local back up of "Alfred.alfredpreferences", even if it is corrupted
2. A copy of time machine backup of "Alfred.alfredpreferences" before it is corrupted; you should have it as long as you have time machine turned on before Alfred wipe out all settings.
What you will need to do:
1. Pick the "Alfred.alfredpreferences" file and enter time machine
2. Pick a time when everything was wroking fine, say a week a