Flushing a container filled with air, with CO2 will mix the 2 gases. Because of the slight pressure increase the excess gas mixture is being forced out. It takes a lot of CO2 to flush that container to get anywhere near 95% CO2, which means there's still 5% air mixed in, and since 21% of that air is oxygen, roughly 1% of that gas mixture is O2, our nemesis after fermentation has ceased.
Best is to fill container with Starsan and push it out with CO2. Needless to say, no air should be allowed to enter. That way your container will be 100% filled with CO2, no air, no oxygen, at the (small) cost of your container's volume worth of CO2.
There are quite a few threads on this here already.
As @kh54s10 said, why exactly do you need to use a secondary?
OK, saw your answer. Most books and instruction sheets are sheer wrong. Secondaries are rarely needed. Only long term aging/conditioning such as sours and perhaps after adding fruit for a TRUE secondary fermentation the use of a secondary is warranted.
Read more HBT, less (old) books.