Hi Francis,
I was previously refining a structures used phased (mlhl) refinement at 3.4. My dataset has a resolution range up to 2.5. The I/sig is still good at 3.0A. I tried changing the resolution cut off in the refinement .def file refinement.xray_data.high_resolution to 3.0, but I now get the error: Sorry: R-free flags not compatible with F-obs array: missing flag for 1 F-obs selected for refinement.
How were the R-free flags generated? We don't have utilities to easily manipulate R-free flags. Assuming you have an mtz file, based on the iotbx/iotbx/examples/mtz_free_flipper.py example script it wouldn't be difficult to find that one pesky reflection and assign it 0 or 1, as you wish. If you send me your mtz file I'll help out. Ralf