HI EmmaHannay ,
Thank you very much for your question.
I am not really sure what you are asking? To replace a BOM item within a product should be a straight forward thing.
I am confused with your last question. What do you mean going through 1 by 1? You mean for orders already created?
if so, I am not sure we have already tested this. let me know if this is the issue and I will ask my external guys to test it.
Pavel