I have a hunter and have the same problem.
2 of my armours in storage still have the extra slot,
my equipped armour and helmet are missing the slot.
The helmets in the storage still have the extra slot.
Shoes and cloak have all slots in the storage and inventory.
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but problem is known: https://www.bungie.net/de/Forums/Post/261131377?sort=0&page=0 ITEMS AND WEAPONS [spoiler] ITEMS AND WEAPONS • Seasonal Trials of Osiris weapons earned through Trials reputation ranks are missing masterwork slots. • Multiple hand cannons no longer have a scope visual. • Artifice armor pieces may be missing their seasonal mod slot. [/spoiler]
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It’s noted as an issue in TWAB and is happening to some artifice armor and not others. It is an error.