Xschem loads the entire raw file to annotate operating point data.If you run again simulation xschem will continue to display the previous data. This is expected and desired behavior, when simulation is finished you can update annotation with 'Simulation-> Annotate Operating Point into schematic. If you need to remove the raw file check that you are not setting 'set appendwrite' as this will append data to the file, and when annotating operating point data xschem reads only the first OP dataset found in the file.