我的同事已经添加了这个代码，似乎它的工作。它不仅在开始时检查空字符串，而且删除它并将正确的数据写入新文件。
这个解决方案似乎很慢，如果可以做任何改进，请告诉我。

private static File skipFirstLine(File inputFile) {
    File outputFile = new File("skipped_" + inputFile.getName());

    try (BufferedReader reader = new BufferedReader(new FileReader(inputFile));
         BufferedWriter writer = new BufferedWriter(new FileWriter(outputFile))) {

        String line;
        int count = 0;
        while ((line = reader.readLine()) != null) {
            if (count == 0 && line.equals("")) {
                ++count;
                continue;
            }

            writer.write(line);
            writer.write("\n");
            ++count;
        }
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }

    return outputFile;
}

对于这个问题没有快速简单的答案，但可以说您应该了解如何将输入视为流。我已经更新了您的“检查空行”方法，从本质上说，它将流推进到第一个“<”字符，然后重置流并停止处理

//it appeared on knt/151 file, so empty lines in the beginning of the file that caused fatal error
private void checkForEmptyLines(BufferedInputStream fs) throws IOException {
    // Set mark and allow for up to 1024 characters to be read before this mark becomes invalid
    fs.mark(1024);
    int ch;
    while( -1 != (ch = fs.read()) {
        if( '<' == ch ) {
            fs.reset();
            break;
        }
        else {
            fs.mark(1024);
        }
    }
}

public String[][] parse(String path)  {
    String[][] table = new String[8][6];

    File data = new File(path);
    FileInputStream dataStream= new FileInputStream(data);
    BufferedInputStream bufferedDataStream= new BufferedDataStream(dataStream, 1024);
    checkForEmptyLines(bufferedDataStream);

    DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
    DocumentBuilder dBuilder  = null;
    Document doc = null;

    try {
        dBuilder = dbFactory.newDocumentBuilder();
        doc = dBuilder.parse(bufferedDataStream);
    } catch (SAXException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    } catch (ParserConfigurationException e) {
        e.printStackTrace();
    }

    doc.getDocumentElement().normalize();
    NodeList nodeList = doc.getElementsByTagName("Data");

    int rowIndex = 0;
    int columnIndex = 0;

    for (int i = 0; i < nodeList.getLength(); ++i) {
        if (i > 7 && !((i - 14) % 7 == 0)) { 
            Node node = nodeList.item(i);
            String line = node.getTextContent().replaceAll("\\t+", " "); 
            line = line.replace("\n", " ");

            if (columnIndex >= 6) {
                columnIndex = 0;
                ++rowIndex;
            }

            table[rowIndex][columnIndex++] = line;
        }
    }