When I tried to convert large EML files with attachments, I had this problem. The process kept stopping and failing in the middle. The first thing that worked was splitting the email into smaller parts instead of converting them all at once. When you use other apps in the background, it makes things worse because large EML files require a lot of memory. I also looked at several large EML files by myself to ensure they weren't broken. Some were and the conversion stop working.
I tried many other tools, but when I switched to GainTools EML Converter, I found that it worked better with large files. It crashed less often and finished the conversion without missing out any files.

Visit here: https://www.gaintools.com/eml/