Hi Lovepreet,
The .bnn files are binary formatted data files associated to USRBINs. These can be plotted in the Plot tab of Flair by clicking Add → USRBIN and then browsing for the .bnn file you want under Binning detector. After selecting the file, the binning info will then automatically display the USRBIN definition as you included it in your input file. Is this what you mean by recovering the input?
The .bnn files can be converted to readable ascii text files by using the → ASCII button on the Run/Files tab as shown in this answer. It is then a simple matter of only selecting the data columns you want to plot (i.e. getting rid of the header text block) in MATLAB or any other language.
Best regards,
Andreas