Hmm... that's odd. About the only other explanation I can think of is that your Palm somehow corrupted the data files on the card when the battery got low - this would be pretty strange, though, since PlecoDict always opens files on an SD card as read-only and hence it shouldn't be possible for them to be altered. Or possibly the preferences were corrupted and it was trying to access the cards from the wrong directory - did you try pressing the "Reset Prefs" button on the "No Dictionaries Installed" screen?
Regarding the flashcards, there's a slight chance you may be able to recover them - go into c:\program files\palm\(your username)\backup and see if there's a "PlecoDict Flashcards" and/or a "PlecoDict User DB C-E" file in there. If so, try installing those two files to your Palm - there's a chance that they may still be the old versions rather than the new ones that were generated when you reinstalled. For future reference, with an SD card problem you don't actually need to delete the software before you reinstall; just reinstall and that should replace the problem files without affecting your flashcards.
You can back up your flashcards in the future by going to that same backup directory (c:\program files\palm\(your username)\backup) and copying those Flashcards and User DB files to another location on your hard drive - that should keep them safe against future reinstalls.
And actually it was only midnight in New York, I'm not sure why the clock got that one wrong... perhaps something to do with the recent daylight savings time switch.