From my experience, my hemoglobin levels have always been consistent for long periods of time, except during pregnancy. I used to run 10.1-10.2. Now in my 40's I'm running 9.3 all the time. However, I definitely had and have times of what I would call flare ups that don't seem to be related to the numbers. Definitely your body can be using resources to maintain consistent values during higher stress times. So even though the numbers aren't moving, stuff behind the scenes is being affected.
It's interesting to me that the three girls in my family who have the same beta-0 gene have totally different symptoms and Hb levels! Also, how some people in the same family with the same affected gene have thal-minor, while others have thal-intermedia. Obviously there are other things at play that affect thalassemia. Based on my experience, tests, research, etc., I think a lot of it comes down to oxidative stress - which also probably has a lot to do with other difficult to diagnose/treat conditions like fibromyalgia and lupus. (I know there are better tests for lupus, but I've heard of someone testing negative for the antibody after lifestyle changes when they'd tested positive for years before that. That's not supposed to happen.)
Since the lab values in my family have traditionally not fluctuated so much, I don't have a lot of insight there. But I wonder if you take note of other things going on at the testing times if you could start to identify things that possibly cause enough stress for your girls' little bodies to not be able to keep up with Hb and RBC production. If you could pinpoint anything, you might be able to help boost them during those times with certain foods or supplements.