I created a door with a window made from Colored Block Clean and reduced the opacity. I placed the door inside a frame made from same block but solid color. I painted the frame with the brush and when door reaches fully opened state the frame blocks become invisible. If I remove the color by resetting the default brush color, the blocks remain invisible. Replacing the frame blocks makes them visible again.
Hard to explain but I did take screenshots.

Also, water and particles not visible while looking through moving door.

Can you send me the screenshots?

Can't post them here right?

Initially I thought it was caused by placing the door offset to the grid so I made another following the grid and got same result. I don't have any screenshots of the water and particles disappearing but that should be easy to recreate.

It can't be Optifine related because I don't have it installed.

Oh by the way, it seems to be only the blocks that are touching the hinge side of the door.

Will be fixed in the upcoming update, which should be available tomorrow. Thanks for reporting this issue!!!