In order to guard against players accidentally storing or selling items that belong to gear sets, we will be placing a mark on the equipment icon for items that are registered to gear sets.
This feature will be implemented in patch 2.1, and as you know thiis is coming real soon, so hang in there just a little bit longer.
Also, though there are generally only a few cases where items are missing from a gear set, we are planning to display something along the lines of the below confirmation when equipment is replaced:
The “XXXX sword” registered to this gear set cannot be found in your Armoury Chest. Would you like to replace it with a different piece of equipment?
(Replace) (Search) (Cancel)
If you select cancel, it won't change your equipment.
If the main weapon for a gear set is missing, we feel that as long as we can avoid situations where the gear set has to be deleted, then it will be okay to change equipment in other slots normally and update the gear set.
In addition to these adjustments we are proceeding to make other minor improvements to gear sets and retainers; however, it's a bit difficult to show our plans with only text on the forums, so once everything is finalized I will be sure to share with you all.