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I've never bottled without laying the bottle (or jug) on it's side for 30 seconds to several minutes. I have a rolling rack right beside my bottling station. It has several shelves (big commercial baking sheets, about 18" x 28"). I use 2 or 3 shelves to stage onto. If working alone I then move them to set upright on the top of my 2 freezers. There they get labeled and priced. Once cooled some get boxed back up, others get set down into one of the freezers. I have 2 such freezers, one has 1/2 gal only and has shelves. As a row gets filled up, a new shelf is set right on the top of the jugs and a new row is started. The HG has 3 layers when full. The other freezer is qts, pints and half pints. Qts go in the deep end and everything else in over the raised compressor part. Qts have 4 layers, pints and half pints only 2 layers.
I bought those freezers at a yard sale about 10 years ago for $40 for the 2 of them. They are the type you used to see in mom & pop stores with ice cream novelties in them. Turned out to be a good investment. I shut them off mid- late October and turn them back on about May 1-15.
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The other thing i do during the bottling process is to mark them with the year and the boil number on the bottom of the bottle. For example - 20-9 would be the 9th boil in 2020. This inventory process allows me to better track production and provides a good record if a quality control check is necessary.
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Never had one leak!! and we mark them with batch #, year, barrel, grade and name after they have cooled. We send syrup all over the U.S and even have shipped some to the Philippines. Our syrup has made it all the way to Hawaii and Alaska even England. PS my wife said tighten the cap up. If it's leaking, It's not hot packed.
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We lay all our filled bottles on their sides for at least 30 seconds before standing them up. OMSPA recently did research on molds found in maple syrup and this was one of the recommended best practices, if my memory is correct.
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Do be careful. I used to lay them all down until the batch was done, then stand them all up. Last spring I had some caps that would soften with the heat and after a few minutes on their sides, there would be a pop and the cap would fly off and syrup would start flowing out. So now I fill and cap a bottle, lay it down, then stand up the one done before it. Takes a minute or two to fill and cap each bottle, so the one prior had more than enough time on its side to sterilize the cap.
Resist the urge to re-tighten the cap after standing the bottle up. The softened cap can stretch and pop off the threads and you need to start over.
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We always lay ours on there side and there are times they sit like that for days. I understand the concern of space, it does become an issue.
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We lay them on their side as well. Does take up a bit more room but I don't leave them like that for longer than the bottling session. I've found the only issue I've had with leaking was self inflicted. Filling too high to the brim didn't allow much room for any changes which wouldn't allow the seal to hold. Now I'm diligent to leave just enough room at the top for expansion with the heat.
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Years ago I took a maple class from Glen Goodrich. And what he was teaching was once you capped the jug to turn it upside down and than back and place it standing up. I have done that for 20 years never had an issue and I have open jugs that where 3 years old and never found mold. But its clear that one way or another you need to sterilize the air space.