Ships 2.0 and multi-encounter battles

Kerrigan

If a ship that was a reinforcement survives a wave in a battle (or a battle in territory wars), does it keep the benefits of the reinforcement ability for the next battle? If not, why not?

Many of the new reinforcement abilities completely change the gameplay surrounding those ships by adding permanent effects (for example: command shuttle, silencer, sergeant, ahsoka). By placing those ships in the reinforcement slots, it was determined that having them act as reinforcments rather than as front-line ships was more beneficial.