When we launched the new inbox, we made a few changes that might effect the way your inbox are organized.
We migrated over all of your Direct Messages and Group messages into a single new inbox, but organized them into threads so that everything is super easy for you to find. Your sent messages, rather than appearing in a separate folder, will be added to a thread. The change to threads means that some messages are consolidated, so might appear to have moved, or it may appear that you have less messages than you used to. But, they're all there, just reorganized!
* Note that one type of message was not migrated over: "Broadcast" messages, an outdated way to contact your followers that hasn't been available for two years, was not migrated over. After analyzing the content of these messages and finding that most were self-promotional, we opted not to migrate these over as it would reduce the quality of your messages.