I too am unsure as to what your asking, I felt this was worth reply with because I can tell you tried to clearly express your problem. Try cutting out the content from the scripts that you can get working, ask a more targeted question, "Why does this script not do this ________", or a more open-ended question, "How would you do this," but make sure your objective is clearly laid out.

Take notice to the gramatical parsing required by your statement:

If the ids are not the same, I don't want it to write anything to the final file unless one of the ids was blank, but I do want to write them if they are the same, such as:

That writes out as
if (id1 != id2) { !write_to_file unless id1 = '' && unless id1 == id2 } ## WTF!!!!

Which is just as easily written as I want to write to output only if an id is blank or if both correlate to each other
if ( id1 eq id2 || not defined id1 || not defined id2 ) { write_to file() }

Which screams to me, dump both of them in a sql table and do a full outer join
Lol, good luck to you...