I've cleared all cookies and started fresh in Cookie several times. After clearing the cookies, I log into Zendesk and Harvest, and favourite any cookies that are created. After a bit of time to make sure no other session cookies were saved, I'll quit and relaunch Chrome, but then find that I have to sign back into Harvest plugin again. It's not a full sign-in (Harvest account & PW), but click on sign-in. That cookie seems to persist.
@shak cookie needs permission from macOS to access any files on your computer. So resetting this will cause Cookie to ask again, before it can do anything… ie removing or reading any cookies on your computer.
It’s quite safe to remove the permissions. all that will happen, is all your browsers will be disabled . You won’t lose any of the favourites or settings, you will just need to give cookie permission and re-enable your browsers.