If you want to edit existing keymap items, you should use wm.keyconfigs.active. This ensures that your addon can override the currently active keymap in Blender.
You should also disable a keymap item (and add your own via wm.keyconfigs.addon) instead of modifying it.
wm.keyconfigs.user is a bit hard to work with. I recommend to avoid using it to add or modify keymaps.
This example searches for a specific keymap based on traits like its identifier, type, value, and modifier keys. If a keymap is found based on the criteria, it gets disabled and added to a list (so you can re-enable the keymap item when the addon is unregistered).
import bpy
disabled_kmis = []
# Find a keymap item by traits.
# Returns None if the keymap item doesn't exist.
def get_active_kmi(space: str, **kwargs) -> bpy.types.KeyMapItem:
kc = bpy.context.window_manager.keyconfigs.active
km = kc.keymaps.get(space)
if km:
for kmi in km.keymap_items:
for key, val in kwargs.items():
if getattr(kmi, key) != val and val is not None:
break
else:
return kmi
def disable_shift_s_snap_kmi():
# Be explicit with modifiers shift/ctrl/alt so we don't
# accidentally disable a different keymap with same traits.
kmi = get_active_kmi("3D View",
idname="wm.call_menu_pie",
type='S',
shift=True,
ctrl=False,
alt=False)
if kmi is not None:
kmi.active = False
disabled_kmis.append(kmi)
if __name__ == "__main__":
disable_shift_s_snap_kmi()
# Register your own version of Shift S with click drag
# just like you would with any addon hotkey.
...
To re-enable the disabled keymap items when the addon is uninstalled:
def register():
for kmi in disabled_kmis:
kmi.active = True
...