I do not know a specific tool to merge mzXML. But it looks like the xml schema http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd is not really complex. It should be possible to write a few lines XSLT 2.0 an transform the multiple mzXML inputs to one mzXML output using the Saxon-HE transformer https://www.saxonica.com/download/download_page.xml.