The flare is the bit where, as you say you stop the aircraft descending, yes this takes a little energy and will bleed a little speed off, but normally the approach will be at Vs + 1/3 so once the flare is complete then you will still have plenty of speed in hand above Vs and ideally you will then hold off until Vs+ a couple of knots.
The amount of the flare required to arrest the descent will be to some degree dependent upon the amount of descent. If you have an EFATO, you will be gliding at a steeper approach angle, and perhaps with less opportunity to establish a good glide speed. As I have mentioned, the 182 amphibian, at 3350 GW likes a glide approach at 80 KIAS, and 12 degrees. That's a lot of "down" to accelerate to level. Thus, there could be much more energy used, so you complete the flare much closer to stall speed, which is okay, it'll just result in a rather brief hold off phase. I certainly have done power off landings where no hold off was done, flare, and you've landed.
The point is to understand that the flare is the portion of the landing where you trade your stored energy into acceleration upward, to arrest the descent. Did you store enough energy for that?