Hi if as you say the system was flushed then NO BROWN WATER OR RUST should have been left in the system ! What did he use to flush system?? Was it a proper high power flushing pump ? what chemical was used in flushing pump to clean system ? was an inhibitor used after cleaning ? did he clean out the expansion tank ? How long did it take to power flush system ? this system would take a min 4/5 Hrs if very dirty should have put a pre-clean into system for at least 7 days, as you see quite involved to do a full system flush, I take it these are qualified people you are employing ?? Note do-not change pump unless system is clean, you will just push rust around system untill it blocks up or damages other components