Marking SMS messages as read/unread or deleting messages not working in KitKat

Solution 1:

With Android 4.4, several things have changed with regard to SMS. Among them is the fact that only the app that is registered as the default SMS app has write access to the provider.

Check here for a short blurb on changes to SMS.

Check this link for a more in depth look. This one explains what criteria your app needs to meet to be the default messaging app.

And here's the official fun stuff.

So, if your app is not the default messaging app, that would be why the specified functionalities have stopped working.

A possible workaround for the default Provider restriction can be found in the answer here.