
Quoting
Mr. Knowitall
The statute you cite speaks to a presumption of a break in continuity of residence based upon an absence of more than six months. An absence of less than six months doesn't create the presumption. Two trips of less than six months won't trigger the presumption, although I wouldn't be at all surprised if she's asked about the trips. Although if she's been continually in the U.S. since 2000, they may no longer be particularly interested or concerned.
Given that it's 2009, she either applied for citizenship back in 2001 or she did not - but there's no way to retroactively file by January, 2001. (Did you mean "after"?)