My common strategy is no do not flip one of the led lights when they are SMD components. In fact, it is not possible to solder them again if you turn them upside down, as the solder pads are just in one side. So the solution is to modify the board to reroute the current as needed:
First of all detect which is the positive lead of the led, and this must be connected to the current after the resistor. Then you have to isolate the negative lead and this will be connected to the white and yellow wires from the decoder.
One easy way, and with no danger, to detect which is the positive and negative side of the led is using a tester or polimeter in diode or conductivity mode. This is the mode where it beeps when current is passing without resistance. Touching the led with the tester pliers will make it light slightly when in the correct place. This is the red plier in the positive lead, and black plier in the negative one.
Here you have indications showing where I cut the cooper tracks (3 places, in red) and were to make a bridge between tracks (blue):
I used in this case a DH05 decoder form Doehler & Haass, purchased at decoders.es:
And that's all, no need of sanding or making place in the shell as this decoder fits well in the position you see in the photo, and if you reroute wires properly: