Same or confusing PDF names mostly happen because many MSG emails have blank subjects, the same subject lines, or copied file names.
I would handle it like this
- Keep only final MSG files in one clean folder.
- Remove duplicate or unwanted emails before conversion.
- Do not save the PDF output inside the same source folder.
- Keep a separate folder for converted PDF files.
- Test a small group first before converting all emails.
Softaken MSG to PDF Converter is a good option for this task as it can convert MSG files in folder mode. It also allows you to select the destination folder to save the converted PDFs. It also keeps attachments separately, which makes checking the output easier later.
Run the free demo on a few MSG files first. You will quickly see whether the PDF names and attachments are coming in a manageable way or not.