I don't think anythink would dissolve RTV silicone sealant, but Toluene might be worth a shot.
Arcturius: tell us more! Is this a thick layer of silicone goop, or is it conformal coating?
Keep in mind that toluene might dissolve a number of other plastics on a motherboard, including the PCI slots, the IC chips, the CPU socket, etc... I would like to think that they are safe, but can't say for sure.
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