I have copied mtz file to a new file with a lower resolution limit using the "Reflection file editor” tool. I copied all arrays to the output file. When I attempted to continue refinement with the new mtz file, a message appears saying that there are no R-free flags in the mtz file. Yet, the new file contains the R-free-flags column but the values are inverted, 1 is changed to 0 and 0 is changed to 1. In the output option dialog the box “Preserve original flag values” was checked.