It seems that this is a common issue suddenly. Every month people post that they have issues regarding the NPC equipment. (not necessarily on these forums..)
The issue is often that people seem to convert the item_template to item.dbc. Item_template does not contain all item entries that item.dbc contains.
For this reason, replacing the original item.dbc with a generated one will usually lose data which leads to problems.
Not all items in the game are accessible to players. This is why not all items have data in item_template. The items that are not available to players may not have damage or other such stats (or we cannot read that data).
These items are cosmetic and used by NPCs. Let's say for example that there is some special item like a lantern that guards use. For convenience, the NPC equipment system uses item entries from item.dbc. This lantern may not be available for players since we don't want them to use lanterns, but the displayid and such data must be associated with the entry through item.dbc.
What you can do is to add only your edits to the item.dbc or you can extract the data you are missing from item.dbc to DB so that the converter has all the needed information.
I think the easiest solution would be to try convert the item.dbc into an SQL which uses INSERT INGORE. That way you can make a copy of your item_template, run the item.dbc sql to it and then generate the dbc file and then delete the DB table that contains the dbc info for extraction purposes.