How can three quarks contribute mass to as many as 540 protons without violating conservation of charge?

It's hard to know exactly what you're getting at here. The (alleged) new atom has only 118 protons in it's nucleus.

If you want to know how a quark can contribute to the mass beyond it's own mass value one has to understand in the atom, the sum is composed of the whole of its parts - and their arrangement or alignment.

An atom's mass is tied to energy levels. Smaller particles like quarks serve as channels or 'stewards' of the protons energy and, therefore, contribute to its mass.

Protons can be envisioned as variable wattage light bulbs with three filaments. Depending upon the switching arrangement each filament absorbs more or less energy. In this analogy the quarks would be the filaments. Two up quarks and one down quark in each proton.

Each quark has a variable (MeV) mass capacity and their mass varies at any given moment according to the rest of the structure of the atom, however, combined with the gluon mass that holds them together, create the proton's 938.3/c2 MeV.

When you envision these things as wave form packets, expressing polarity within a greater field, it makes more sense. The waves carry subharmonic charges and these are orbiting in the proton like a hot potato being thrown from one quark to another increasing or decreasing each of the quarks current MeV. The gluon mass is the greater field holding these quarks and is why the majority of the proton's mass exists here. Despite all this movement of energy, however, the charge is confined to the proton.

Hope that helps.