When two identical capacitors are connected after one is charged, the total energy in the system decreases due to energy loss mechanisms such as resistance and radiation. In ideal conditions, there is no energy loss, but real capacitors exhibit losses, which can be modeled with resistors in parallel. The energy stored in the charged capacitor is calculated using E = 1/2 Q^2/C, and when connected, the charge divides equally, resulting in a new energy state of E = 1/4 Q^2/C. The discussion also draws parallels to harmonic oscillation, emphasizing that without energy loss, the system would oscillate indefinitely. Overall, the energy after connection is less than before due to these losses.