Duplicate files can appear when many MSG emails include repeated attachments or small signature images. Since the tool supports common attachment types like PDF, DOC, XLS, PNG, ZIP, HTML and TXT, you should test a few MSG files first and check how repeated file names are saved in the output folder.
Do not save everything into one common folder if the MSG folder is large. Keep the output arranged by email folder or batch. Then check repeated file names separately. To handle this safely, use the safest tool like Mailvare Free MSG Attachment Extractor for extracting MSG attachments without changing the original email files. when you want to extract MSG attachments in a more controlled way without altering the original emails.
Use the demo first on a small MSG folder where repeated attachment names are already present.