It does pull from vault, it does Not put back into the vault. Some things are a technical problems that require more effort to find a workaround.
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Are you on PC or Console? If any of my items are in the vault, I get an empty slot with a yellow exclamation point and have to manually pull it from the vault on PC.
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Others in the Clan have reported the same on PC
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Unless you are saying you have to have open mod slots on character because it can not replace anything, then that would make sense as I do have my slots full most of the time. Either way though, it is easier for me to still use DIM and needs investigated with a workaround to allow gear to be put in the vault to make it worth using imho