This problem is so common, and I have tried a lot of converters for converting EML files into MBOX format in bulk. I would suggest using BetaVare EML to MBOX Exporter, it works best for me. It converts multiple EML files at once without any data loss and also provides accurate results in just a few minutes. It retains all my email details like metadata, formatting, and structure, etc., in its original form after the conversion, and it also maintains the folder sequence, which makes it easy to find the files. You should definitely try this software.

For more information: https://www.betavare.com/eml/mbox/