All Lincolns after 1917 should have the initials. Sometimes due to
Die Deterioration or excessive die polishing the initials are removed from the die. 1989 is well known for missing initials but it happens in other years as well. In 1989 some dealer did a big promotion on the 89's and pushed the price up to $8 - $10 per coin. After he sold out and the promotion ended the price dropped back down to nothing.
The initials don't disappear due to filling of the die because the initials are raised on the die. You would have to fill most of the bust to get rid of them. I suppose sice they are raised they could chip off the die but I've never seen a case of that.