You can absolutely accomplish this without affecting any of your VMs. If I understood you correctly, you need to move some volumes's ACLs from ESX0001 (vcenter created igroup) to VMFS01-09 igroup and another set from ESX0001 igroup to SQLVMFS01-09 igroup. The easiest way to accomplish this is to go to each of the volumes in the array GUI, click "Edit" and navigate to the "Security" tab on the right. This will have a listing of all the ACLs for that volume. You can add the new and correct ACLs and remove the ESX0001 ACL from the list. This will ensure that going forward only the right hosts will be able to detect those volumes. Word of caution, though. Before you make these changes, make sure the hosts that aren't supposed to see the volumes have them disconnected. Otherwise you'll have hosts looking for volumes they can no longer access.
Hope this helps!