Acceptance testing validates that a system meets its requirements and determines whether it can be sufficiently trusted and put into operation. For cyber physical systems (CPS), acceptance testing is a hardware-in-the-loop process conducted in a (near-)operational environment. Acceptance testing of a CPS often necessitates that the test cases be prioritized, as there are usually too many scenarios to consider given time constraints. CPS acceptance testing is further complicated by the uncertainty in the environment and the impact of testing on hardware. We propose an automated test case prioritization approach for CPS acceptance testing, accounting for time budget constraints, uncertainty, and hardware damage risks. Our approach is based on multi-objective search, combined with a test case minimization algorithm that eliminates redundant operations from an ordered sequence of test cases. We evaluate our approach on a representative case study from the satellite domain. The results indicate that, compared to test cases that are prioritized manually by satellite engineers, our automated approach more than doubles the number of test cases that fit into a given time frame, while reducing to less than one third the number of operations that entail the risk of damage to key hardware components.