Maintaining a constant high level of Free T3 can cause bone loss, but if you split your dosage throughout the day so your FT3 level stays constant and within its range, it shouldn’t be a problem.
If you split your dose, taking 1/2 in the morning and 1/2 in the afternoon, you won’t be spiking your FT3 like you are now. Yes, it will go up temporarily, but won’t stay there, as T3 reaches its peak within a couple of hours after taking, then starts declining.
There are ways you can help regenerate bone tissue… taking calcium, vitamin D and magnesium supplements, maintaining a good diet and normal weight, exercise, etc are all ways to help prevent bone loss.
BTW - always be sure to postpone taking thyroid medication until after having a blood draw, since the labs will show falsely high Free T3. It’s important to be consistent (do the same thing every time you have blood work), otherwise your results won’t be consistent since some will be false highs.
It won't really make that much difference for your bones because you'll be getting the same amount of T3 over the day, anyway. That said, it's almost always better to split T3 medications into multiple doses during the day because it keeps Free T3 levels stable vs taking it all at once and having FT3 spike, the drop out when the medication is all used up.