If you reinstall Warzone 2100 over the top of a previous installation (like you would in an upgrade scenario) all the files in the \Warzone2100Portable\App\Warzone 2100\ directory are deleted and then reinstalled. This normally wouldn't be an issue, but that's where the sequences.wz file is stored so all the cut scenes (high or low quality videos) were blown away when the directory was purged. Normal users are going to wonder "what happened to the cut scenes I downloaded?". Not good. The installer needs ignore that file if present and preserve it.
The links to the high/low quality video downloaders are broken and dump users into the main portable apps file area on SourceForge. It did that same thing earlier today, but the downloader was near the top of the list so I just manually downloaded it. Now it looks like the two files don't exist on SourceForge anymore.