1

my partner shook my fermenting cider while I was at work will this affect it it was about day three. smelled sweet not like vinegar when I bottled it.

2

Shaking brings yeast back into suspension. It has negative effects on clarity of finished brew, but on the other hand it helps yeast to ferment all available sugars. Most important in strong beers. In weaker brews, ones at 6% ABV or less, both effects are pretty negligible.

As long as water from your airlock didn't make it to your cider, it should be all right.

  • In the early days of primary fermentation I shake my stuff. It doesn't hurt anything and not even clarity really. Once you are well into secondary fermentation is when you probably don't want to shake it anymore. – Escoce Nov 23 '15 at 15:33

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