Since Helix Ultimate 2.0.3 update you can override overrides of component views from a template.

To achieve it you have to create new folders using this schema: templates/{template_name}/overrides/ - then inside put CORE component or module view override.

For example, if you decide to override the single article view created by Helix Ultimate you should:

1. Create the following folder structure (use File Manager):
    templates/shaper_helixultimate/overrides/com_content/article
2. Then copy the default.php file from:
   a) plugins/system/helixultimate/overrides/com_content/article
   OR  if you want to customize the original article view then copy a file from here:
   b) components/com_content/views/article/tmpl
3. Now you can edit & customize the default.php file without fear that the next update will overwrite your changes.

How to Override Component View

If you want to override the extra installed (additional) component view follow the below steps. At first, check if your component wasn't overridden already inside the template folder in /html/com_NAME folder. As an example, I used SP Simple Portfolio, a single item view.

1. Copy file from: components\com_spsimpleportfolio\views\item\tmpl\default.php
2. Using File Manager (component or FTP tool) create new folders here: /templates/shaper_helixultimate/html/com_spsimpleportfolio/item
3. And upload inside the newly created folders default.php file.
4. Now you can edit & customize the default.php file code without fear that the next update will overwrite your changes.
5. Do the same steps for other component views.
6. Instead of File Manager from step 2, you can use the built-in Joomla tool (Templates - Templates (Site) - click Template Name - click "Create Override" and find component and view that you want to override.

How to Override Module View

The procedure is very similar to the component view. Just different resource and folder structure. At first, check if your module wasn't overridden already inside the template folder in /html/mod_NAME folder. If NOT please follow the below steps:

1. Templates - Templates (Site).
2. Click into template name, for example, Shaper_helixultimate.
3. Then click the tab "Create Override".
4. Find the module that you want to override. Click on its name.
5. Notice! All module views would be overridden by this procedure. If you want to override only a single view - you have to do it manually.
6. Now you can edit the module file, for example, templates/shaper_helixultimate/html/mod_spsimpleportfolio/default.php.
7. You can customize the module file(s) without fear that the next update will overwrite your changes.