The legacy MoFlo and Cyan produce FCS2.0 files from Summit v4 or less which are analog (FCS2.0) files.
Analog data (or FCS2.0) data files are read by FlowJo in the format they were exported. Analog data files are exported with data scaling information and compensated fluorescence values (if compensation was done on the instrument). Therefore, all FCS2.0 data read into FlowJo will appear exactly the same as it did on the acquisition instrument. As the software cannot manipulate FCS2.0 data due to the stringent analog standard keyword convention, little can be done to rescale or adjust the data once it is acquired.