Is there risk of off-flavours from the gunk at the bottom of the secondary? Or is it mostly the primary that has this concern if left too long?
Keegan
There is no risk of off flavors, even when you primary for up to 4 weeks. Secondary fermenters are merely a vessel used for clearing beer and/or aging for long periods. This can easily be accomplished in a bottle with similar results.
Check out this article. Someone was kind enough to send me the link a few days ago during a similar discussion.
The differences are so subtle, the participants were split down the middle as to whether or not flavor improved or suffered from racking off the yeast. In fact, there have been a few threads on here where brewers mention leaving beers on the yeast for months at a time with excellent results. Some brewers feel the yeast improve the flavor, others like a secondary. In the end, it's all a matter of preference since differences seem virtually undetectable.
Also, an excerpt from "Brewing Classic Styles" by Jamil and John Palmer:
"In general we recommend a single-vessel fermentation for a minimum of 1 week, and not more than 4 weeks, before packaging. Racking to a secondary fermenter is not recommended except for beers requiring a long fermentation, such as lagers, or beers requiring a second fermentation, such as sour ales and fruit beers."
Conditioning for most beers can take place in the primary, then refining in the bottle. A lot of brewers bypass secondary entirely, myself included. Of course, this is dependent on style as referenced above.
Search around on here, there's a lot of info on the topic. For example,
this. And more recent research (listed above) is good to know.
