When the Flint 2 is operating in Access Point Mode, NAT and DHCP are disabled, and the device mainly works as a Layer 2 access point/switch. Client IP addresses therefore need to be provided by the upstream router. Simply re-enabling the IoT or Guest SSID in LuCI only enables the wireless interface itself. It does not automatically restore a separate subnet or DHCP service for that network.
If you would like to keep separate IoT and Guest networks while using the Flint 2 as an AP, the upstream router needs to support VLANs and provide the gateway/DHCP service for each VLAN. The Flint 2 can then be configured as a VLAN-aware AP, with the corresponding IoT/Guest Wi-Fi interfaces mapped to their VLANs.
You can refer to the following examples:
Flint 2 + AP Mode + upstream VLAN/DHCP