There is no need on SaberSim to upload a new updated entries file for every Late Swap you run. Once you've downloaded an entries file from a Late Swap build, we will store those new entries and assume that you uploaded that file to the sites, and those will be your new active lineups. If you come back to Late Swap again later, we will Late Swap against the most recently swapped lineups, keeping everything in sync. You can see here, I've run multiple Late Swaps for this particular slate, and this will track throughout the slate perfectly.
Now, if at some point throughout the slate, this becomes out of sync, typically either because you edited lineups directly on the sites, or outside of SaberSim. Or built Late Swap lineups, downloaded those entries, but then never uploaded them to the sites you'll need to start over with a fresh entries file. You should re-download your current entries file from DraftKings or FanDuel. And then, on the Entries tab, use the upload new entries button to upload that entries file and get everything back in sync.
If you have any other questions about the rest of the Late Swap process, or lineup building process on SaberSim check out some of our other videos in our Support documentation. In the meantime, thanks and good luck.