Using a small flame, heat the seal till the folds melt away. It is often helpful to "tease" the glass by giving VERY LIGHT flutters of air. This is sort of like having a bubble at the end of a straw and moving it go back-and-forth but not letting it leave the straw's tip. You are trying to maintain the general wall position and NOT making it move significantly back and forth. If you blow too much, you will force more glass to get involved, the more glass you get involved, the uglier the seal will become.
Also, be aware that the longer you heat the glass, the more it will start to drip downward. It is best to maneuver the seal so that the area you are working on is either pointing up or down. This way any glass movement will be in place and less likely to drip downward creating a thin area on top of where you are working and a thicker area on the bottom.
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