As the title states, when i try and delete a blueprint, either through the game repair option or manually, it destroys my entire structure. It shows the blueprints as supporting existing objects, even when they aren't built in any capacity.

This literally just happened to us in our game. I've been building a mega base high up next to the hot dog cart, been building for days now and all of a sudden, after misplacing a blueprint, I went to delete the blueprint and the whole structure fell to the ground. I'm not the one hosting this world so the host reloaded the previous save and the structure was back, he ran over to try to get rid of the blueprints via the game repair option and once again the whole structure fell to the ground. After again loading a previous save we started looking at all the blueprints and they all say they are supporting 700+ things, which doesn't make sense. Even ones that are clearly above other objects and not connected to anything are saying supporting 700+. 
The most interesting thing is this was not happening yesterday at all. We all were working of different base builds and had to remove blueprints, and nothing was destroyed. Now all of a sudden today we have this bug. Very weird, and annoying.

I’ve had that bug randomly appear. Most of the time exiting the game and coming back in fixed it. I did have that glitch remain stubborn one time despite reloading multiple times so I just started building a few sections over and suddenly I could delete the blueprints that have been acting like they were supports. The game definitely gets confused once in a while about which pieces are supporting what.

ive had this happen as well. took many times of reloading the save to before collapse of the base to notice that somehow they supporting foundation had shifted to a different one and adjusting anything on this new one caused it all to collapse. i fixed this by adding a new supporting foundation and watched the number of supported items change to the new one.