It's probably had a knock some time and the water drain issue did the rest.
I looked on Servis Pox, you have to buy the whole side of the car...
No-one seems to be doing sills for the 406, so it looks like you'll have to ad lib it

You could either get hold some sheet steel and fabricate a bit to replace the "missing" part, or find someone who's dismantling a 406 and doesn't mind you turning up with an angle grinder, remove the offending section and weld it in (much better than the "cover" sills we used to get, I'm sure they're weak as sh!t and if you had a wee shunt the car'd fold up

).
I suppose it depends just how much sill is missing, any chance of a pic?