I decided to ask the experts what they thought and wrote to the Cornell Lab of Ornithology for guidance:
Thanks for getting in touch and for your concern for sick birds. Yes, this is a terrible year of Salmonella especially on the west coast. Although such outbreaks are known to occur and are something that bird populations can recover from as a whole, in the interest of caution, taking down your feeders for awhile and cleaning them is a great thing to do.
Whenever a sick bird of any kind comes to your feeder, we recommend that you remove the feeders the sick bird is using for awhile to assure that disease is not being spread at your feeders. While the feeders are down, clean them thoroughly with a diluted bleach solution or very hot water, rinse them, and let them dry completely. Once you put the feeders back up, be sure to clean them every week or two. If sick birds return, avoid using feeders with ports that birds put their heads into and clean your feeders at least weekly.
The good news is that it's fine to take a break from your FeederWatch counts at any time, so no worries about that. It is also ok to FeederWatch without feeders! We are trying to spread the word about this, but the name of the project makes it a bit counter intuitive. You can modify your site description so it reflects that you don't feed during some months of the year (it is question #9 on the site description form), and then continue counting, if you would like.
Find more information about bird diseases on our website: https://feederwatch.org/learn/sick-birds-and-bird-diseases/
We wish you many healthy birds. Happy FeederWatching!
Emma Greig, Ph.D.