1) All you need do is pull say, a litre of water out of it every day. That way it will replenish with....a litre of fresh water.......every time you do this.
Is it advantageous to flush out your boiler periodically? I dunno.
You have to ask yourself why you might do this. Yes the water in the boiler is stale, but it doesnt make the coffee, it is only the source of the heat for the heat exchange to the fresh water that your espresso is made with and, it produces your steam. Does it matter if your steam is produced from stale water? I dunno!
2) Dont do that or you will affect the machines ability to produce coffee, steam, and recover, from the way it was designed & built to do so by the manufacturer.
3) This is tangential to your questions however if the boilers capacity is said to be 13 litres then it does not mean the boiler actually contains 13 litres of water! *;) *An espresso machine boiler would generally be set to fill to somewhere roughly between 1/2 and say 2/3 of its total capacity, leaving plenty of room for steam and the ability for the machine to reach proper operating pressure/temperature as a result so as to be able to do the "job" intended which actually is to do the "heat exchange" to the fresh water coming through to brew coffee with!
In any case what I am saying, is there is probably only say 8-9ish litres of water in there but whos counting!