To have ultimate control over your inputs, we suggest using LoadData with a CSV that contains file locations and any metadata you desire to add. Then you can reverse the order manually in the CSV. Beware that CellProfiler runs multi-threaded now, so that if you are running with the GUI and have a computer with multiple cores (most do nowadays) then multiple cycles will be processing simultaneously, so you with the defaults you can’t guarantee exact order of processing. You could go into Preferences and lower the number of cores down to 1 from the default of howver many cores you have, but that would slow processing down substantially. But your order would be mostly how you prescribe it in the CSV.
Let us know how it goes!