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 and 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 start again once you resume.