Issue: new platform install overwrites data in \portableapps [resolved: user error]

It's possible you installed to the wrong path. Frequently, users who reinstall the platform will install to X:\PortableApps instead of X:\ or vice versa, resulting in two separate platform instances, one with their apps and one without. Reinstalling 14.4.3 over an existing install doesn't affect any of the apps within the PortableApps directory. I just confirmed it with a test and there's no code within the installer that would do this.

It's also possible that your disk is having issues. If you suddenly had issues running Start.exe and then had folders go missing on a simple platform reinstall (which is how all platform upgrades are done), I'd consider that drive highly suspect. In other words, it's losing data and will likely stop working soon.

Related Note: Installing the platform over itself is the same way that upgrades are always handled automatically. So, if a user with 14.4.2 selects to automatically upgrade, the 14.4.2 platform will download 14.4.3's installer, run its installer pointing at the current platform location, and close. There's no code in the installer to alter any of the apps in sub-directories within the PortableApps directory, just the PortableApps\PortableApps.com directory. If you're seeing something else consistently, I'd love to have the steps to recreate it to stomp any outlying bug there might be.