Switch (dis)connects an LDO regulator from VBATT. Where should the filter cap go?
C1 is there to counteract the resistance/impedance/inductance of the wires between the battery and the LDO.  Thus, it should always be placed as close as possible to the input of the LDO.

The switch has a small resistance/impedance/inductance, and you would not want that between the cap and the LDO.

Therefore, the cap should be placed as close as possible to the LDO, and the switch goes between the battery and the cap.