Based on your question, I will assume that you are not using the .hex files and hex loader to change the firmware in the new Nano. In order to use the source code and make changes, you will need to have the full uBITX_20 master files in the smae directory, and then open/make a project with the uBITX20.h file as the source.
The above is from memory, so I am sure that there are errors on the file names. The fact that all of the required modules (end in .ino) must also be included in the same directory as the top level source file.
Also, I would first do the compile option to test the compile before doing the download. Again, it has been almost a year since I tried doing this myself, so you would be better off to wait for someone with more recent experience to give you the correct steps.
You can start with the Hex Loader and verify that the uBITX works with the pre-compiled version.