Where is the data stored?

If you are on OS X 10.7.+ (with app sandboxing), then TimeKeeper's database is located at:
~/Library/Containers/com.timekeeperapp/Data/Library/Application Support/TimeKeeper/storedata

On systems without sandboxing support data file can be found at:
~/Library/Application Support/TimeKeeper/storedata

To open ~/Libray folder on your Mac, open Finder and choose menu item "Go->Go to Folder" and enter ~/Library into text field and press Go button.