You can choose the labels to be used in refinement with the keyword "input.xray_data.labels=XXXXXX" (<~ put label name here) in the command line, or by choosing the desired label in the drop down menu in the GUI. So it should not be necessary to strip out additional data columns in the reflection file.

If it happens that phenix.refine (or any other Phenix tool) overrides your explicit input, it would be good to let us know, so we can address the issue.

As already mentioned in this thread, if labels are not specified (= user intention is not conveyed to the program), default behavior is to use IOBS. 

Best wishes,

Dorothee