What's you Exchange server and CU version?
Do all the mails sent from outlook not showing in OWA or part of them? Conversely, can mails sent from owa be synchronized to outlook sent items correctly?
Whether the “Do not save copies of sent items” check box is checked or not? File > Account Settings > Account Settings. Double click your IMAP account and click More Settings. Under Advanced tab.
Also make sure the Save copies of messages in the Sent Items folder option is checked as well. File > Options > Mail > Save messages section
You mentioned that: Tried re configuring imap but issue didn't resolved, do you mean re-configuring the imap profile for the user?
In theory, Outlook won't delete your emails/folders when set the root folder path to Inbox. We may also refer to the discussion in this similar thread: Changed "root folder path" and emails are now missing--can I recover them?
This has just happened to me adding IMAP, folders were not there just disappeared. However try this, very simple and I found it just by accident. Look at the move icon on topbar and you should see your folders listed with (on my computer), however folders are not accessible. Now click on organising and then on new folder for left hand navigation pane. Voila all my folders reappeared with a new folder
In addition, can the mails be found in outlook sent items now? If so, we can use outlook to export the mails. Please also check you have configured any rule may take effect on the sent items.