Hello SachinPerambraGood morning!Thank you for publishing in Microsoft Community. We are happy to help you.Based on the description you have shared; we understand that affected user moving he emails from the Inbox to the Sub folder, the email is getting deleted. When you pulled the audit logs, it showed that the email was deleted by the affected user who moved the email to a sub folder.Typically, when any issue happens about deleting email in mailbox, we use Audit log to find out who deleted the emails. So based on the information you are not sure that the email has been deleted by the user or accidentally deleted the email.
However, to make sure if something else has deleted the email, please kindly make a test once again, send a test email in the shared mailbox and ask the affected user to move the email in the same subfolder, follow the steps of the affected user and check if the same issue happens. and let us know.
If the same issue happens, use another account with access in the shared mailbox in another Pc and do the same thing in the shared mailbox. If the issue happens again let us know. It can be possible that there is some inbox rule or hide inbox rule. Let us know the results.
Please feel free to let us know if there are any questions or if we got you wrong. We will continue to assist you based on the information you provide. We sincerely appreciate your patience and cooperation.SincerelyEben Ezer Tres | Microsoft Community Moderator