There's a difference between removing fan leaves and taking off low spindly branches.
I've never done it that late- I often re-pot at about week 2 or 3 of flower and do it then if I see crap under there.
The low growth has a very very low concentration of hormones in it anyway so it's like the plant isn't as aware of their removal as it would be if you took off a vigorous terminal shoot high on the plant- you know what I'm saying? It's like those low bits are nearly dormant because of the apical dominance effect, adn only really come to life if the higher parts of the plant are removed, or if they get enough light to start growing.

Oh edit- just be sure to take off only the stuff that's pretty obviously pale/spindly/stunted/sickly.