1997 Suzuki Esteem Alighnment and Boot replacement

I have a 1997 Suzuki Esteem with 138,000 miles on it. It runs great. There have been no disturbances in handling, control, or ride -- except I now have torn boots. We ordered the standard replacement boots, but we had it aligned not too long ago. (Front and rear alignment) My question is this: Can I replace both driver and passenger side CV boots without disrupting the alignment?