However, WinSCP apparently is skipping existing files one by one extremely slowly. It skips them more slowly than it downloads them (because downloading can be done for several files in parallel). So on the second day, none of the remaining files are downloaded.
Please let WinSCP get the full file lists from both computers and compare them once with an efficient algorithm (sort both and go through them in parallel), then download the missing files. Don't compare the presence of files one by one.