The unsatisfactory answer is that all your custom work will be overwritten. But there's good news!

Since the launch of Joomla! 1.5, the Joomla! development team foresaw such occurrences and built a presentation override system into the framework as a solution.

What Are Overrides?

Overrides allow you to customise the standard output from any Joomla! Module or Component by adding code to the html directory of your template. This override method ensures that your customisations stay in place when you upgrade your extension (e.g. com_jobboard) to a newer version.

For example, if you want to change the way that the 'Job Details' view displays a com_jobboard job listing, then you should copy the file at

PATH_TO_JOOMLA/components/com_jobboard/views/job/tmpl/default.php
TO
PATH_TO_JOOMLA/TEMPLATE_NAME/html/com_jobboard/job/default.php

You can then customise the file inside the html folder of your template and Joomla! will automatically pick that up and use it to display your "Job Details" view instead of the original one.

You can read up more on this topic at http://docs.joomla.org/How_to_override_the_output_from_the_Joomla!_core