what you need to do is remove ALL the cards from the deck and put them back again
don't just fill in the missing cards. I hope this will fix it for you
*Edit* I believe this is caused by a counter which is still counting 29 cards even after you replaced the missing ones. By removing all the cards because the -1 counter can not count -1, only 0 it will reset.
Next time when you disenchant a card be sure to remove it first from all the decks you have it in.