Yes, you can safely clean multiple duplicate MBOX files from different folders. The best approach is to use SameTools MBOX Duplicate Remover. After removing duplicates, you can split the cleaned duplicate MBOX back into separate files if needed. This ensures all duplicates are removed safely without losing unique emails. This tool supports all Windows OS versions, like 11, 10, 8.1, 8, 7, and also supports email clients without any software or application. It handles a lot of duplicate MBOX files. You can just follow a few steps and remove duplicate MBOX files.

Visit here: http://www.sametools.com/duplicate/mbox/