No.
The upgrade process wants the current home directory untouched, because it's going to be using it and upgrading the data in it.
The Atlassian recommended upgrade path is now "Run the installer, tell it to upgrade, point it at the current installation and wait".
This will clobber some of your settings though, so you'll want to copy those out. The easiest thing to do is before stopping the current Jira, is check the system information page. Look for the section titled "modified files". The upgrade might be breaking all the files named in there. So get a copy of all of them somewhere safe, make a note of where they are, and then after the upgrade, compare the old and new versions of the file.
Note that they can't just be merged - an upgrade I've recently done changed the format of the server.xml file for example, you'd have needed code that could adapt to every change that *might* be in there for whatever reason.
The other option for upgrade is a manual upgrade, where you unpack and build a new Jira and then point it at your existing data. And that includes the home directory. It will upgrade the data and home directory as Jira starts up with the new version, but this does tend to give you even more changed files to edit, as an unpacked Jira won't have any of your changes.
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