The only way I know of is to remove the gsi, deploy, then add it back (updated) and deploy. Kind of pain if there are multiple environments because the subsequent deploys have to roll out in order. We've decided to basically deprecate GSI's. Add new ones, update the code, and roll it out. After confirmation remove the old one if needed. That being said I generally use generic indexes like GSI1, GSI2, GSI3 and take advantage of index overloading.