In a nuclear reaction fission type the total number of protons , neutrons and electrons remains constant
Despite a common belief there is no matter annihilation
The system loses a fraction of the "binding energy "
i.e of the energy which binds protons and neutrons together preventing the nucleus from exploding because of the repulsive electromagnetic force
The Uranium inside the reactor loses aboput 1% mass because it loses a huge amount of energy mainly in form of heat

Protons,electrons and in practice also neutrons are immortal, nobody has ever seen a proton or an electron dying

If so it is not 100% true that matter is energy and energy is matter

I think that to fully grasp the meaning of the equation you must go deeper in the quantum physiscs
In other words even Einstein himself did not fully grasp the meaning of the equation
Thw original Einstein's equation was

dm = L/c^2

if a material body absorbs ( emits) the amount od energy L than its mass increases (decreases ) of dm
Einstein did not claim that matter and energy are the same stuff
It claimed that both energy and matter contributes to the the mass of the body where the term mass must be strictly understood as the "Inertia" of the body

The equivalence mass = matter came from Newton
Since mass was apparentely a constant then mass and matter were supposed to be the same stuff
Same as weight and matter , before Newton

Einstein explained that the Newtonian mass of the equation
F = ma
It seems to be a constant but it is not
Thus you must drop the equivalence mass == matter


In modern quantum physics however , as fa as I know , mass is actually matter but it is not....energy
Energy is something different

The interpretation of the equation is not that easy
you must be really familiar with quantum phisics...I am not, not to that extent at least