Silicone based sealants will burn EPDM rubber roofs. Assuming that you have a rubber roof. If you plan on keeping the trailer long term, I would remove the silicone which usually peels right off. Inspect the roof for visible cracking. If a large amount of cracking is present then your roof has met it's demise. You can prolong replacement by applying an elastomeric acrylic based sealant. Dicor makes this as well as others. This is really just a bandaid until you can do a complete replacement. I have done many of them and if you are at all handy you can to. Kits for a smaller trailer usually range between $500-$800.