This is strange. I have the latest update, and it still works with windowed SSEWas checking Steam to buy it and came across this review by Ariel (3rd Review on frontpage)
The develepor response to it does confirm removal of windowed mode with no plans to add the same, Considering how many Skyrim mods specifically need/ask for Borderless Full Windowed mode, how are u using it, any issues popping up by using game in Fullscreen or is there some way to use Lossless Scaling Upscale/FrameGen with Borderless Windowed Skyrim since PureDarks upscaler does allow that.