An indicator that updates while the settings do not is a desync between two things the controller stores separately, and it is recoverable.
The controller holds the profile configurations in its slots, and separately tracks which slot is selected, which is what drives the indicator. Normally selecting a slot both updates the indicator and applies that slot's configuration. If a profile write was interrupted, or a firmware update rewrote the slot area without updating the selection state, you can end up with a selection pointer that moves while the configurations it points at are stale, empty, or offset by one. Your description of getting profile one's settings while the indicator says two fits an offset exactly.
The fix is to rewrite everything rather than to try nudging it back into line. In the Xbox Accessories app, go through each slot in turn and write a profile to it deliberately, including the ones you think are already correct. That rewrites both the configurations and the selection state. Then cycle through all the slots on the controller and confirm each one actually applies its settings, which you can check with the profile switching test rather than by feel.
Two things to do alongside. Update the controller firmware first if an update is available, because profile storage handling has had fixes and applying one after rewriting the slots can undo your work. And if rewriting does not resync it, reset the controller to its defaults from the app, which clears the slot area entirely, then write your profiles fresh. You will lose your configurations, so note them down first, but it is reliable.
One precaution for next time: write profiles over a wired connection and do not disconnect or power off while the app is writing. An interrupted write is the most common way this happens in the first place.
And keep your profiles saved in the app as well as on the controller, so a reset costs you five minutes rather than rebuilding from memory.
