There’s nothing preventing you from deleting individual automations and Smart Lighting rules unless you have orphaned devices associated with them. In the IDE goto My Hubs and scroll down to the “Devices Found” section. Anything that doesn’t show as either ACTIVE or INACTIVE in the Status column is fair game for deletion. To delete individual items, tap the name in the left column and then Delete. It’s also a good idea to check if you have virtual/simulated devices showing on the My Devices page without an entry in the “Hub” column. If so, assign them one by tapping the displayed name, and then Edit.
If you do decide to delete everything and start over, add back the powered devices closest to the hub first and then work your way out. Powered devices (except bulbs) typically act as repeaters, and will ease discovery of battery powered devices and those devices further from the hub,