All OE quarter glass is sealed with the moulding in place, if you remove it you risk damaging both pieces, requiring a new window.
Heat it up a little with a heat gun until it's pliable and then wedge a stiff piece of wire underneath it, that will hold it up off the body and allow the paint to get behind it. If you've already pulled it free, hope the glass came out too, otherwise break out the wallet.
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