I think you can do all that in one batch render file. Let's say you have file A that contains two reference files (a1.mb + b1.mb) with the correct render setting, you can render that with command and when it finished render, add a second command + the pre-render mel that swap the two references to whatever files you want. You can keep adding that for the rest of your files. No need to save all the files (save space) plus no render queue manager needed.
Example:
render -im a1_b1 fileA.mb
render -preRender "file -loadReference \"a1RN\" \"a2.mb\"; file -loadReference \"b1RN\" \"b2.mb\";" -im a2_b2 fileA.mb
render -preRender "file -loadReference \"a1RN\" \"a3.mb\"; file -loadReference \"b1RN\" \"b3.mb\";" -im a3_b3 fileA.mb
render -preRender "file -loadReference \"a1RN\" \"a2.mb\"; file -loadReference \"b1RN\" \"b2.mb\";" -im a3_b3 fileA.mb
so on....
I haven't tested it but I'm sure it will work.