I don't know if the is was fixed with an update since March, but I have not run into this issue. If I open and read a message on my iPhone, then check my inbox later of my mac or iPad, the message is in the inbox, but shows as read.
All (I also posted this previously on iMore),
to your point, it appears that after years of iCloud email read/unread status not syncing on iOS devices when changed from OS X Mail or icloud.com, that it is beginning to function. not sure if this is new or not, but it got my attention today, as it is (or was?) one the glaring holes of iCloud mail.
Both my iPad and iPhone showed 15 unread emails, as did icloud.com. I deleted all 15 unread emails from my inbox on icloud.com today, and within about 30 seconds, looked down and my iPad's and iPhone's unread status was changed to no unread - the badge disappeared. To my knowledge, I've never seen this happen before. For a long time, when I delete/read emails on an iOS device, it updates on OS X Mail and the web immediately, but iOS devices are left hanging until I manually opened Mail to refresh. Looks like a push request is going to registered devices when emails are deleted, or marked as read/unread.
I tried also to see if the status would update by simply reading an email on icloud.com, but not deleting it. This also worked. Marked the email as read on icloud.com and both the iPad and iPhone badges disappeared after about 10 seconds.
I also marked a read email on icloud.com as read, and it updated its statuses as unread on the iOS devices as well.
Last thing I tried was to delete an already-read email from the inbox on icloud.com while Mail was open on my iPad and iPhone. When I did that, it did disappear from both inboxes on both iOS devices, within a minute or so. It's delayed but it works.
Now if they will only address opaque server-side silent filtering.
Both iOS devices (iPad 3 and iPhone 4S) are running stock 6.1.3, and did the work on icloud.com using Chrome...but the browser choice shouldn't matter. Mail is set to push on iOS devices, not fetch. Fetch interval is 15 min, just for reference.
What do you all see, or not see? Can others try this and post your results?
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I think there are a lot of great reasons to switch from Gmail to iCloud email, here are my top 4:
http://franklinmcmahon.com/2013/03/...-outlook-hotmail-over-to-apples-icloud-email/
I really enjoyed reading your piece on this. I think the ad-free function is overlooked but really important. The thing Apple needs to get right for many to trust it, is to fix opaque filtering. I want to see the junk I'm getting - because Apple might think it's junk, but it may not be.