Yes, you can convert thousands of EML files into PST format at once. For this, you require an automated tool that supports bulk conversion. I recommend that you try BetaVare EML to PST Exporter for converting numerous files at a time with instant processing. This tool quickly converts files with large amounts of data and provides highly accurate conversions. It preserves every detail of the email such as formatting, metadata, content, attachments, etc, authentically during the conversion and also maintains the original structure of the folders. It is compatible with every version of the Windows operating system and has a basic interface that can be easily used with basic computer skills. I had a great experience with this tool; you can also try it for seamless conversion.

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