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Attribute taste variation to volume of bottle?

This is not exactly a home brew question but this site seems to be the best fit in the stack exchange network for it. You can home brew the beer in question with a kit produced by the brewery though ...
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3answers
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Will there still be yeast leftover for second fermentation after filtration?

I want to filter my beer then put it in the bottles for the second fermentation (aka making the beer fizz). I am worried that I will get rid of all the yeast and end up with flat beer.