Dhanraj,
Yes, you can absolutely build your input files outside of the ArcGIS environment. You will have to follow the documentation for the WRF-Hydro GIS Pre-processing tools as well as the WRF-Hydro Technical Description to add the necessary lake input grids and files to your existing routing files. You will need to derive lake parameters from your DEM and build a LAKEPARM file and appropriate lake inputs for the Fulldom_hires.nc file. Essentially, you just need to populate the LAKEGRID variable in the Fulldom_hires.nc file and build a LAKEPARM.nc parameter to describe the lakes. If you can replicate those files using the examples we provide, then the model should be able to simulate your lakes.
It sounds like you have already run the WRF-Hydro ArcGIS Pre-processing tools to build a routing stack zip file. If you were able to run that, then I would think you would also have permission to run the "Add Lake Parameters" tool. Have you tried to start fresh by building a routing stack that includes your lakes from the beginning? If this does not work for you, I can take a look at your files and try to run the "Add Lake Parameters" tool to your existing routing stack. You will need to provide the files via download link through our user request form:
https://ral.ucar.edu/projects/wrf_hydro/contact.
Thanks,
Kevin