Edit
It is important to clarify the distinction between the regular Feb Steam update and the beta program. The issues experienced have been with the beta, and not the standard update.
Original
Since Valve overhauled Steam’s user interface yesterday, multiple users have reported facing serious issues with the application.
The most common problem is that upon opting into the beta and updating their Steam client, some gamers are losing their game files.
Somehow the update causes Steam to lose the installation files for previously installed games. This has resulted in a number of gamers reporting that Steam is detecting the game as uninstalled, and initializing the download from scratch.
It is therefore recommended that gamers avoid installing the Steam update for now. If it is already too late and you are a victim of this problem, then uninstalling your game, and cleaning out all its files from the Steam Apps folder, and then reinstalling the game seems like the best solution.
Discuss your experience with the Steam makeover in the forums