If you are doing the upgrade and keeping all your paths, you'll just need to make sure you have the plugin installed after the upgrade.
If you are changing the location of your JIRA application, you'll need to copy the scripts and set the new location on the plugin. Please see more information about this here.
Hope this helps,
Both the other answers are correct. But to add more detail:
If your scripts are "inline", then they are in the database and will be retained.
If you are specifying a path, and it's an absolute path, they will carry on working. If you specify a path relative to the working directory, and you are changing that, then you will need to update them. Now is a good time to change that, by eg using a relative path that goes above your working directory, or creating a symlink called eg "scripts" under the home dir.
As Jobin says you should test the upgrade first. This is true if you have any plugins you have written yourself, including script functions.
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