To restore the correct order to your data after editing it a lot or marking lines for deletion, choose Edit | Zap ( or Ctrl+Z). This will permanently cut out all lines of data which you have deleted (by pressing Del) unless you've restored them from deletion (Ins).
In the case of a word list, it will also re-order the whole file in correct frequency order. Any deleted entries are lost at this stage. Any which have been assigned as lemmas of head words may still be viewed, before or after saving. However, after zapping, lemmas can no longer be undone.