When you say drain and clean out the system.
He would have to drain the system in order to install the new boiler.
Cleaning the magnet is not cleaning the system.
There should be no gunk in a system with a new install, as all the gunk must be cleaned out, otherwise your warranty can be void, and it will damage your boiler.
There are different methods and views on cleaning but the end result should always be a clean system if it's not this would be deemed a bad install and fiitting a magnetic filter is not a fail safe as it doesn't pick up all of the particles on the first pass.
The clean out took nearly all day and a huge tank of black stuff was taken away. Our rads were old but he said they were fine no need to replace them although we were prepared to buy new rads. Apparently the black comes from the rendering down of metal surfaces within the rads and is an ongoing thing. More residue was expected so he put in a magnet. I dont know the rights and wrongs of all this just telling it as it is.
If you started another thread with the title should my system have been flushed and cleaned, you would see what I mean by the response you would get