Parsing of bnf file removes quotes about ponyge2 HOT 1 CLOSED

The behaviour is expected, otherwise you would not be able to do many things in grammars.
You need quotation to be able to include the separator symbol | or empty productions "". Actually every terminal symbol should be in quotes as well as whitespace, but the parser allows to use whitespace and other symbols without using quotation out of convenience. This means the following two productions produce the same output:

<expr> + <expr>
<expr>" + "<expr>

The following production is different, as it does not have any whitespaces:

<expr>+<expr>

You can use single quotes to include double quotes and vice versa. So for your grammar, I would suggest the following solution:

<src> ::= '{"Ns": [3, '<es>']}'
<es> ::= <ds>, <ds>, <ds> | <ds>, <ds>, <ds>, <ds>
<ds> ::= 1<d> | 2<d>
<d> ::= 0 | 1 

BNF can be represented as a BNF. Single and double quotation is needed to do this. See the rule <literal> as example

from ponyge2.