You're doing it wrong. MHX uses ExtData not UserSaveData. You can use SaveDataFiler (switch to Ext tab) or extdata_dump: https://gbatemp.net/threads/3ds-extdata-dump-and-restore-tool-extra-data-editing.378492/Could you implement an option, where you can import a backed up save, as both Save Manager nor svdt are able to backup and inject MHX savegames and your tool is able to do backup.
... but I do plan on adding that functionality at some point.