I doubt that the 400mm f/5.6L qualifies as a 'flagship-type' lens - that would be the 400mm f/2.8L IS that is being updated right now.
Note the words used are "popular flagship lenses" - I'm uncertain whether the 400mm f/2.8L is one of Canon's popular lenses.
My thoughts on lenses which I think are natural candidates for replacement:
A. Long non-L primes: 85/1.8, 100/2, 135/2.8, and 200/2.8 II.
B. Special lenses: TS-E 45mm & 90mm, MP-E 65mm f/2.8.
C. Misc lenses: 100-400/4.5-5.6L, 28-135/3.5-5.6, 35/1.4L, 17-40/4, 24-70/2.8L.
D. Wide non-L primes: 20/2.8, 24/2.8, 28/2.8, 28/1.8, 35/2, 50/1.8 II, and 50/2.5
IMHO, Canon will not upgrade any of the lenses in group A, because they are sharp, and because any upgrade will make the upgrades compete with the similar L lenses. Between lack of popularity and lack of competition, I'll bet canon will not upgrade any of the lenses in group B.
My 2 cents is 3-4 out of the 5 lenses in group C will be upgraded, and a new ultra-wide lens will be announced to compete with the Nikkor 14-24 and Sigma 12-24. With the already announced 500mm & 600mm lenses, that makes 6 lenses.
This makes me wonder about 2012 - with group C practically emptied in 2011, and group B being small, would Canon start replacing the lenses in groups A & D in 2012 ?