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 ago
3. Roll back to that file, but don't let it override your current one. A new file called "Alfred (original).alfredpreferences" will show up in the same folder
4. Now create a new folder called "Alfred" in your Dropbox root directory (really just make a new folder somewhere, but creating it within Dropbox is recommended by Alfred)
5. Drag your newly created "Alfred (original).alfredpreferences" into the "~/Dropbox/Alfred" folder you just created, and rename the file to "Alfred.alfredpreferences"
6. Follow this instruction https://www.alfredapp.com/help/advanced/sync/ to change your sync folder to "~/Dropobx/Alfred" you just created
7. Alfred should restart and all you preferences will be back.
Hope it helps.