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When you specify an external properties file to use, the file gets completly overridden and you lose your custom settings.  The new external properties file just has the following...

# Last modified by Liferay IDE Wed Feb 20 09:38:31 MST 2019

include-and-override=[some location]\portal-ide.properties

I believe the problem is in the LiferayTomcatUtil.java class with the _setupExternalPropertiesFile method. The current code wipes out my settings.

Current code...

private static File _setupExternalPropertiesFile(File portalIdePropFile, String externalPropertiesPath) {
        File retval = null;

        File externalPropertiesFile = new File(externalPropertiesPath);

        if (FileUtil.exists(externalPropertiesFile)) {
            ExternalPropertiesConfiguration props = new ExternalPropertiesConfiguration();

            try (InputStream newInputStream = Files.newInputStream(externalPropertiesFile.toPath());
                OutputStream outputStream = Files.newOutputStream(externalPropertiesFile.toPath())) {

                props.load(newInputStream);
                props.setProperty("include-and-override", portalIdePropFile.getAbsolutePath());
                props.setHeader("# Last modified by Liferay IDE " + new Date());
                props.save(outputStream);

                retval = externalPropertiesFile;
            }
            catch (Exception e) {
                retval = null;
            }
        }
        else {
            retval = null;
        }

        return retval;
    }

When I revert the code back to the following, it works.

private static File _setupExternalPropertiesFile(File portalIdePropFile, String externalPropertiesPath) {
        File retval = null;

        File externalPropertiesFile = new File(externalPropertiesPath);

        if (FileUtil.exists(externalPropertiesFile)) {
            ExternalPropertiesConfiguration props = new ExternalPropertiesConfiguration();

            try (InputStream newInputStream = Files.newInputStream(externalPropertiesFile.toPath())) {
                props.load(newInputStream);
                props.setProperty("include-and-override", portalIdePropFile.getAbsolutePath());
                props.setHeader("# Last modified by Liferay IDE " + new Date());
                props.save(Files.newOutputStream(externalPropertiesFile.toPath()));

                retval = externalPropertiesFile;
            }
            catch (Exception e) {
                retval = null;
            }
        }
        else {
            retval = null;
        }

        return retval;
    }

Notice how the output stream is not created in the try statement as in the current code.  When it is created in the try statement, it does not work.