You don't say what device you're using, but did you have some sort of reset occur on your device at some point before your magic plant disappeared? The loss of progress in the game is usually due to a crash or reset when the game hasn't been saved recently. As with most handheld applications, the game is saved only when you exit (e.g. to the launcher). If you leave it running all the time and then have a crash or reset, the next time you launch the game it will load the last saved state. That may be from before you discovered the Flower of Knowledge.