You're ok
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From what I understand, if you go to a secondary fermenter that can keep some potentially unwanted flavors from seeping into the beer, but all that stuff will settle out and you should be ok. But, going to a secondary will increase your risk of contamination, and some guys say it is absolutely NOT neccessary. Also, be sure not to go to the secondary to early, maybe around one week.
1-2-3 rule of thumb: 1 week in primary, 2 weeks in secondary, 3 weeks in bottles.
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