You can't remove, but you can replace as you said. Once you replace a Gem, that Gem that was replaced is gone. So I guess, if you want to sell the item, you can do either of these:
1. sell the item with no upgrades
2. add Gems to upgrade it, then sell it
3. add a Gem (let's say Glacial Gem), but then replace it with Fire Gem, which makes the Glacial Gem lost. But then I don't think you can remove it, so you have to sell it with that upgrade.
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