I found the plant of knowledge last night and it was in the lower left of my nursery most of the day today. Now its gone! Game stats say 0 of 4 discovered. :-(

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.

could be I guess. I use a Treo 650 and it did have a crash from Zlauncher early afternoon. But I have Plant tycoon running from an SD card so whenever I exit the app/switch to another program, it copies everything back to the Card.

Anyway, in an effort to try to prevent this again I wanted to make a copy of the save game. Problem is I can't find a file that would be the saved one - what is the name of the file??

The Palm versions of the earlier games do not create a savegame file, but rather store the game state in a way that's not directly user accessible. The only way to back up and recover your game progress is to use a backup program that will allow you to save "unsaved preferences." There is a thread discussing that situation here.

LDW now creates a separate savegame file for their games, starting with Village Sim on the Palm platform and all of their PPC games.

Ok I suspected that when I couldn't find a file 'owned' by Plant Tycoon. I use a program called Cleanup to do just what the thread says. Is there a certain preference I should watch for or just back up all unsaved preferences that are listed?

To be safe, you should just back up all unsaved preferences.