Dear Jinkai,
Right now there is not a very good system to do this.
The easiest option is to remove the SQLite database file and restart Collect Earth with a fresh and clean database that will be automatically generated by Collect Earth. DISCLAIMER: IF YOU DO THIS YOU WILL OBVIOUSLY DELETE THE DATA ALREADY ON THE DATABASE!! So in that case remember to export the data so that you keep a copy of everything you had there.
The database file is called collectEarthDatabase.db and is located in the hidden folder : C:\Users\YOUR_USERNAME\AppData\Roaming\CollectEarth
You can access easily this folder by clicking on Tools->Open Data Folder

This will open a file explorer where you can locate the collectEarthDatabase.db file. Before removing the file close Collect Earth (as otherwise the file will not be able to be removed as it is in use of the application)
Once you have done this you can restart Collect Earth and a new and completely empty database file will be automatically created created!