Here is a quote from the FinCEN faq's issued on August 29th: "You also should not maintain the list of named subjects for the purpose of evaluating whether to open or to conduct a transaction, unless specific instructions accompanying a 314(a) request state otherwise."
I think this may be the point of confusion, and why people say not to retain the lists. However if you look at the italicized portion it seems, IMHO, that you can--without fear of breaking with compliance--retain a list if you do not use it for purposes other than documentation of conducting a search.
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