You can import MBOX to IMAP while keeping the folder structure by using a method that transfers emails folder by folder, instead of merging everything into a single mailbox. Manual syncing methods often flatten folders or mix emails, especially when dealing with large MBOX files.

A simpler and more controlled approach is to use a direct solution like the MailConverterTools MBOX Converter Tool. The process starts by adding your MBOX file to the software, where the complete folder hierarchy is displayed in a tree view. This lets you see and select the exact folders you want to import, ensuring nothing gets misplaced. After selecting IMAP as the destination, the tool uploads each folder individually to the IMAP account. During the import, it preserves original folder names, subfolders, email dates, sender details, and attachments. Options such as previewing emails, removing duplicates, and applying date filters help maintain accuracy and prevent errors.
Read more: https://www.mailconvertertools.com/blog/upload-mbox-to-imap/