The Sony is pretty standard reader, though they all have their peculiarities.
You should probably be ok bringing them over, but without seeing the files it can be hard to say for sure. Just keep copies at each step and when it goes caflooey, you just go back a step and try again, probably wishing you had taken up model railroading or some other hobby.
If both books rely on stylesheets, then you can compare them and bring over anything that is missing from your final one's stylesheet. It is when you don't use stylesheets that you will spend forever fixing each instance of your styling.
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