It’ll be fine, just don’t stress it too much. I’ve repotted mine a bunch and they always have fruit on different stages. Make sure the roots stay cool (low 70’s) and shaded, make sure the soil isn’t dry (give it a good soak a couple of days before). If you loose some roots make sure you trim back the same amount of leaves to minimize transpiration stress, and wouldn’t put it back in the hot dry sun for a while.
Root pruning is a bit different, doing some research on bonsai posts will prepare you better for that task.