Are pecked berries harmful?
We were picking blueberries and a couple of birds were having a grand time pecking away at the rows. We were trying to avoid the pecked berries and managed to get a nice bucket and discarded a few with pecks that accidentally got into the bucket. We washed and froze them for the winter. Some members of our family think this is fine, some think we should only use them in pie or bake them so the temperature would destroy any 'leftover' germs, and others don't want to eat them at all. Can you actually catch a disease from birds if they get in the berries and you eat the berries (after washing them)? The berries we kept had no pecks or feces on them. I rinsed them in running, cold clean water, though the fear is 'some of the bad ones touched the good ones and something could have rubbed off,' and that 'there were birds sitting/standing on the berries/plants.' We would be eating them thawed without cooking them.
Actually this food safety issue is not just limited to blueberries. All produce needs to be sorted for quality and cleaned. OSU Extension recommends that produce be rinsed in cool, running water and use friction from your hands to remove any dust and dirt. Blueberries bumping or rolling around against each other in your sieve or colander, could also count as "friction." Your description sounds like you were very careful and thorough. There could be very small amounts of dirt and/or pathogens left on produce, but it is within human tolerance levels. The benefit of eating fresh or preserved produce far outweighs the risk if you follow the basic cleaning directions outlined above.
Additionally, we do not recommend adding soap or bleach to cleaning water or using produce "washes" that are sold in some stores. The produce "washes" have not been shown to be more effective than rinsing in cool, running water with friction, so are just an added, unnecessary expense.
For more information on freezing produce see Freezing Fruits and Vegetables (https://catalog.extension.oregonstate.edu/pnw214).
You and your family might also be interested in You Can Prevent Foodborne Illness (https://catalog.extension.oregonstate.edu/pnw250), which describes washing fruit.
Enjoy your blueberries!