What purification changes
Purifying a recovered item adds it to the permanent armory so it can be selected for later loadouts. Until that bridge is crossed, a strong mission pickup should not be assumed to be a permanent starting option.
Loot comes from exploration, elites, bosses, and mission rewards. During a hunt, a newly collected item can immediately replace the equipment in its slot. Back at Sanctus Clypeus, the permanent collection is managed at the Loadout Station, while the Blacksmith improves chosen weapons and armor.
Permanent versus run-only progress
Purified gear, persistent upgrades, unlocked equipment, applied character experience, and collected lore scrolls can survive across runs. Nexus Boons and other temporary effects expire, while failure can also remove completion bonuses, acquired consumables, a portion of Souls, and equipment not secured through the mission’s progression points.
Efficient priority
Prioritize purification by how much an item expands the armory, not only its current number. A new weapon type, defensive alternative, or effect that enables a different Boon synergy can be more valuable than a small improvement to a crowded slot. Once an item is permanent, invest Blacksmith resources only when it supports a loadout you expect to reuse.