Digital Pigeon resumes uploads by splitting large files into parts and upload each of the parts separately. Once all parts have uploaded they are joined back together into a single file. If you pause (or interrupt) an upload, Digital Pigeon will start from the last completed part an then upload all remaining uncompleted parts.
By default, the part size is 50MB (you can configure this under Manage > Transfers > Multipart part size). If you pause an upload before a single part completes, it will start from the beginning once you resume.