Gas Hot Water Tank Flue – Gap as it Passes through Roof Deck
There is up to a 1/2” gap to the outdoors between the circumference of the water heater tank flue and the gasket going through the roof deck.
Can I caulk this with High Temp Caulk or is the gap there for a reason?
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Is this gap in the thimble, as in you can see sky through the gap? That's a problem -- you don't want rain getting in, but you have to use a proper assembly here. If the "gap" is just insulation, then it's probably not a big enough gap -- you typically need at least a 1" gap to combustibles around the typical B vent vent pipe from a gas fired water heater.
There is info in the link I posted in your previous question regarding the proper way to air seal around a vent pipe like this.