We all know the recent patches have attempted to screw over private servers.
Well then blizzard, let the battle begin, you will not beat me without a fight.
Heres how i easily solved the problem with the ? Marks.
The process is called canabalizing,
Step 1. Find the item you wish to eliminate the ? Mark.
Step 2. Find the item that you used for it's display id.
Step 3. Change the entry id of your custom item to that item's entry id.
Step 4. Delete or change all drop chances, vendoring, or crafting of the item if you wish.
Done! The process will consume the old item, however your new item will be fine.
NOTE: There are tons and tons and tons of items that will never be used by players in private servers, so its fine to destroy a few.
I am sure I am the only one who has discovered this so far, i've known about it for awhile and eventually got sick of seeing ugly question marks in other private servers that i had to post this. Stop the pain, Canabalize!
ADDED BONUS TIP:
TO ENCHANT CUSTOM GEAR, HAVE SOMEONE ELSE ENCHANT IT INSTEAD! (Does not work with enhancments like Leg Armor etc.)