Re: 'All Our Yesterdays' theory
. . .Just to name two off the top of my head: maybe the act of preparing phasers shorts out some key component immediately; perhaps the Atavachron is based on certain theories of physics in which values assumed to be physical constants aren't really constant. . .
Building off this idea, we can go further. We don't know what "preparing" actually does. Perhaps preparing weapons insures they are operable only within the time frame where that technology is available. A .45 pistol might work until a certain point in the past. If phaser technology was never invented on the planet, they might not work at all after going through the Atavachron.
Dr. Howard, Dr. Fine, Dr. Howard: For duty and humanity! --Men in Black (1934)