Removing Bootstrap completly

There's nothing to be gained from removing Bootstrap from a Bootstrap based Template.  That's like buying a Porsche and removing the Porsche engine when you get it home.  What are you going to replace it with?  A VW engine?  In that case, just buy a VW. 

Nancy

An anti-tank missile would be my preferred weapon of choice but I suspect you want something left of your server, in which case to remove Bootstrap you would have to remove ALL of the site files/components that use Bootstrap, then use some other workflow to build your site.

It's not as simple as clicking the mouse and getting rid of it.  It's a structure to how you website operates.  You would need to rebuild your site from the ground up.