Can't say it is a problem I have come across myself...the odd bit of chipped paintwork yes

but I would very much doubt that you would scratch UPVC window frames or sills with the bristles of any of the brushes.
And certainly not painted wooden window for sure.
Sill are always the first to suffer from weathering though, the scratches she thinks she has seen may only be marks the bristles have made in this weathering, and not scratches at all.
when you go and look at he job, have a cloth and a little non abrasive cream cleaner and give a sill a test clean using it...or at least a patch on the sill so that you can then highlight the fact that it is not in fact scratches.
Also have your applicator along with you, scrub with soapy applicator too, this way you will aslo know if it is a problem you can correct by going over the sills trad.
Using an applicator means you can bring a lot more pressure to bear (conversely this could also be said to increase the risk of scratching

)
If it is just weathering, use of applicator should make only a marginal difference
[this I know because a customer last month asked me to give her sills a really good scrub as she thought I was leaving them dirty, was a bungalow, the old dear had cleaned some of the sills but couldn't reach them all.
After giving them a real going over with WFP I then went back over them with that scrubby bit on the applicator...didn't make a whit of difference, but as I found out that she had gone over some of her sills with a cream cleaner that was hardly surprising!!]
But the cream cleaner
will make a difference on the weathered sills.
Should it prove to be this then you can point out the fact that you have not indeed scratched the sills.
There is little you can do to halt weathering...it happens!
you could offer to clean her sills using an appropriate cream cleaner, but you would have to charge her for that service.
But smile politely, don't get involved in arguements with her, and go around to check out what she is saying...it's also very good customer service to do so!
Ian