You have several options to handle existing files. These options can be found under the Advanced options:
You can migrate the content in an existing folder hierarchy and then choose one of the three options:
1. Add suffix to existing files
For example: File.doc will be migrated as File(1).doc
2. Skip exiting files
3. Overwrite existing file.
If you need any further assistance, please feel free to contact us at firstname.lastname@example.org