Hi -
There are many changes in function and data structure from the 2.5 version, so you should definitely upgrade with your Moodle installation. If you upgrade your Moodle to sub versions, you should also upgrade your plugins to those stop points. So, if your Moodle goes from 2.5 to 2.9 and then to 3.4, upgrade your plugins to their 2.9 versions as well.
The questionnaire uses Moodle's standard upgrade process, which is designed to manage the data and ensure no loss or corruption. So as long as you do things properly with the upgrade process, you should be fine.
That said, it is software, ans surprises can happen. You should always do a test upgrade on a non-production copy of your site first, and then verify everything went fine. Then make sure you keep a backup of your production data before you do the main upgrade.
mike