While modifying a ship, I used the Boolean modifier to create a hole on the side of the ship. When I clicked applied there was a massive lag spike, and fearing a crash undoing the past two hours of work, I saved the file
Without seeing the file, my first guess (seeing all those verts) would be that you had subdivision surface modifier on when you tried to apply the boolean.
Apply your booleans first, and then add the subdivision modifier afterwards.
Note - You can retrieve old versions of your blend file after a crash by going to File > Recover > Autosave and selecting the first file listed that contains the proper file name. It’s usually more up to date than selecting File > Recover > Last Session.
Did you use the eye to cut your boolean? Geometry was just messed up…
Instead, I took a cylinder and used knife project…deleted half of the eyes and replaced the mirror modifier…