“Pruzbul won’t work in Yemos Hamashiach because it only works for Sh’mittah D’rabannan, not Sh’mittah D’oraisa.”
You are confusing Prozbul with Heter Mechirah, which does rely on the fact that Shmittah is D’Rabbanan in our times according to most opinions. When Prozbul was created, we were still observing Shmittah D’Oraita as the Temple was still standing; it will therefore continue to work when the Third Temple is in operation.