Downloaded new r4 wood program but old pokemon game memory deleted?

1. Did you checked to see if the WOOD R4 copy you added is meant for your flash cart? Note: there are 3 versions of WOOD R4 by YWG, each
meant for different carts.
2. There might be a need to delete the wood r4.sav (it's a save file generated by wood r4.nds to save it's settings).
3. Try using POKEGEN.exe or POKESAV.exe (find these program via GOOGLE) to read the pokemon pearl's save file via computer.
If the program shows your pokemon are there, then the save file probably not read by WOOD. If they're missing, then likely the save file
been overwritten when run on the new WOOD copy or corrupted.

If they're simply un-read by WOOD (as in still there when viewed through POKEGEN/POKESAV) then they are in tack/safe. But if via any of those program you can't view it no more, then likely it's been overwritten by accident or corrupted, which of cause no way to recover.