Boiler manufacturers require that the system is cleaned to BS5793 before the new boiler goes in.
Adding a chemical before replacement is one of the ways covered by the BS. If that route is taken then the following procedure must be used.
1. Add the chemical and leave the system working as normal (including heating) so that the chemical circulates througout the system. Drain after the chemical makers recommended time (normally between 5 and 10 days dependent upon the make).
2. Isolate water to the f and e tank, drain the system from ALL available drain cocks and open all radiator vents to allow air in and water out.
3. REPEAT AT LEAST ONCE MORE. If the water looks clean during the SECOND drain-down then the boiler swap can go ahead. If it still looks dirty the procedure MUST be carried-out again and again until the water runs clear.
You can see that this will take at least two weeks and three visits prior to the boiler swap itself. In my opinion (and these are only my opinions) VERY FEW boiler engineers will take the time (or be able to charge for that time) to follow that procedure to the letter. However, if it's not done and the boiler maker can prove that it hasn;t been done like that (which is debatable) then they might, just might, refuse to honour their warranty.
More importantly, and I have to point out my bias here, following the above method will eventually remove the magnetite (the small bits of rust that turn the water black/grey) but IT DOES NOT remove the larger bits of rust because the flow of water just id not enough to pick the larger pieces up.
If you phone the tech support for the make of boiler you are going to have they are extremely likely to recommend that a powerflush is done because it is the best way to clean the system. I have come colleagues who do not powerflush before boiler installations, but then they don't have the equipment anyway.
As far as causing problems, I agree with the prevsious post. It may uncvoer existing problems but better it does that when a plumber is actually on site. We have done over 800 powerflushes now and have uncovered pin-hole leaks on radiators in 4 or 5 cases.
Hope this helps.
P.S. Always fit a MAgnaclean or a Y-strainer. Condensing boilers are low water content boilers with small pipework with the heat exchanger. They are VERY fussy about the water going through them. Do not fit a Spirax Mganaboost - they are rubbish.
As above, all that shows is that it wasn't done properly.
BG give a lifetime guarantee on powerflushing so they just need to ring them up and get the to come back and sort it.
FYI, British Gas definition of "lifetime" is as long as you keep paying them for your service contract. They are usually much more expensive than even the very best specialists.