rg, there may or may not have been a vertical airmass movement contributing to the altitude increase. What the BEA reports show is that the nose up command was made and for a period of time, sustained.
The faster your fly, the more force (up or down) a given control deflection will apply to your lift versus gravity vector summation. A number of the heavy pilots on this board have pointed out how gentle control inputs ought to be at high speeds and high altitudes.
Let's say you and I are travelling at 180 knots, and I make a control deflection of the elevator of an inch in a T-28B Trojan. (Built like a Grumman F-8-F Bearcat, more or less, high performance WW II fighter).
Nose moves a certain amount, I pitch up, airspeed will change, I'll trade energy for altitude at a certain rate.
Then, let's say we are traveling at 300 knots, same altitude, and I make the same control deflection. The resulting force will be significantly higher than the one I made at 180 knots. I am likely to get more nose up and much more altitude traded for my airspeed, unless I make a quick countercorrection. If I am used to flying about at 180 knots most of the time, I may put in what "feels" to be the same input in at 320 knots, and get a significantly different pitch attitude. (heh, you may ask how I learned this ...
for another time).
Most enlightening has been some of the explanations in the past few pages of how the control laws in some FBW aircraft sense G load or set G load to govern and control control surface deflection to achieve "X" peformance. Part of the reasoning behind that seems to be to prevent overcontrolling, per my illustration above.
With that in mind, consider the following: what if the most common hand flying task undertaken by a modern pilot flying FBW aircraft is the takeoff or landing configuration and airspeed range. What "feel" is he used to? That seems to be an industry wide concern, at least on the pilot side, if what I read on PPRuNe is any indication.
Then here's the kicker: is FBW "feel" a good indication of what the aircraft is doing?
(That's been addressed as well, some pages back). Regardless of whether it is or not, pilots develop a feel for their aircraft. It's part of being human. Our senses inform a great deal of what we do.
Back to your question.
If you get turbulence and updrafts, you will "feel" its effects in your seat and your body, but often you can't rely on "feel" flying to counteract it, particularly if you aren't flying via visual reference. In that case, you have to deal with it using instrument flying skills regardless of what you feel, or what you don't feel.