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Evevning @ricm
Instead of a using a filler (I am presuming you mean something foam based) how about trimming a small piece of the skirt you have spare and sliping it into the gap? I dont know if the skirt will hold up if you screw tighter but something solid between the decking boards and the skirt would work well and the eye wouldnt notice so much. I have small gaps around my deck, the weather does have a play with that (mine are timber) with yours that are more stable I would just work out the largest bits and leave the smaller gaps.
Dave
Hi @ricm
Firstly I 100% agree with both @Dave-1 and @EricL and finish the new deck to the pump enclosure. Then I would rebuild the door shorter so it will open over the new deck. Yes it will be a step down to the equipment, but aesthetics wise I think this will be the better finish.
I also agree with @EricL and would pre drill more holes and insert additional flat-headed screws in those areas that have gaps to the eco-deck. Then with any remaining gaps I would use an exterior flexible filler as the gas will definitely change with weather.
Nailbag
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