Where is custom.css in the generated html file from nbconvert?

If your sole problem is this line: <link rel="stylesheet" href="custom.css">, you can modify the template file and write a custom HTML exporter:

Navigate to the source directory of nbconvert. Go to ./templates/html/. There will be a file called full.tpl. This serves as the template for your HTML file. Open the file with a text editor and delete the <link rel="stylesheet" href="custom.css"> line. Save the file with a .tpl extension (fullcustom.tpl). Make sure you save it in the same directory as full.tpl.

The next step is to either write a custom exporter class in Python(recommended). You have to inherit the HTMLExporter class defined in ./exporters/html.py. You can follow the procedure described here: https://nbconvert.readthedocs.io/en/latest/external_exporters.html

Now, if you do not want to spend the time doing this, a quick "kludge" would be to actually modify the HTMLExporter class. Create a copy of the html.py file if you want as it is being modified. Open ./exporters/html.py and find the following method in the HTMLExporter class:

    def _template_file_default(self):
        return 'full.tpl'

Change return full.tpl to the name you saved your modified version of full.tpl with (fullcustom.tpl).