I don’t know that you can completely disable the LR, but in Zwave-js-ui Settings > Z-Wave you can change the default radio configuration from USA (Long Range) to just USA (assuming you are in the USA).
S2 and LR are two different things, though. S2 is just a security level. LR is a different communications protocol that does not use mesh. Unless you have changed any of your devices to LR, they are not LR. If your device is connected through LR, the Zwave icon in zwave-js-ui will be purple instead of blue, the device numbering for LR begins at 256, and there will be no beaming available as LR does not support mesh.
I’m not sure if that helps, but I doubt LR is your problem.
Have you updated the ZST39 Firmware?