I have already taken care of deleting those extra appearances we needed to get rid of them due to it will always use the first one found and the second one will never be used. and of course the items would not beable to take the second appearance if it was suppose to have it so that is taken care of.
i ran that command on your server bear with me on this I dont know much about sql really.
at first it looks as if these items have the same id number most of them twice but that don't make sense i thought a record has to have a distinct number? if i look at the items table using the id of the item from that query i only see one record.
I did look at them in the item editor which is quite nice btw

it does show me 2 items but that is because it is looking it up by name and there are tons of items in eq2 which have the same name but a different soe_id because it is a different item.
like the work boots you mentioned that is a heritage quest reward that is the same name but different for every armor type there is a cloth,plate,leather version of it but it also has different stats i think depending on it too not 100% been awhile since i seen that item in game. not only that but it also has a different item for it because you can place it in the house and some of those types of items have the same name others have Trophy:itemname.
The first few items in that query have the same name but are 2 different items one is the incomplete version of the book and the second one is the completed version. all of these have different soe_ids looking at them with the item editor.
Trash loot can have the same name but will also have different soe_ids because depending on the lvl of the mob the body drop. bat fur , gnoll fang etc will be worth more the higher the lvl also there are rare body drops that are worth more then the normal ones they also can have the same name but will be labled fabled