When she kicks an egg out of the nest, it is bad. It may be fertile, but went bad for some reason. How does she know this? Only Mother Nature knows for sure. But you can take it to the bank that she is right.
our would roll eggs out periodically and not take them back. We would then candle them to see if they started or not. most times they did not start. Then again she was sitting on them in Jan with some cool temps about -20C and when see got off to do her things. The eggs must have gotten two cool and died as when they were to hatch we let them go an extra couple days and nothing. When the DW went to check she did not have to fully remove the hen when she new that there was a problem with a few by the smell.
she has 6 eggs under her and hasnt kicked any out yet. its still early we will see. iv had good luck in the past years with broodys hatching eggs . even though this is a different rooster this time.
My broody sat on 5 eggs at first. I candled at day 7 and tossed 1, left the other 4. She sat on the rest until they started to hatch, once 3 were out she kicked the last away. I kept putting it under her for a day then gave up and cracked it open. It was a quiter around day 5 ish. They just know.