probably a 10cm wide slit in the floor has no structural significance. possibly less depth in cm might be sufficient, depending on the ground construction. of course, it's annoying when the architect is also your assessor. a second independent opinion would definitely have been better.
what of course is absolutely not acceptable is the floor height increase. in new construction under no circumstances! I might consider something like that for 30,000€, but not for the small amount of money they might possibly pay. then rather a new base slab, although that won't be necessary here.
incorrectly installed pipes occur quite often.