Are you running the command-line upgrade or the web-based upgrade? If you’re using the web-based upgrade, I’d suggest running the command-line upgrade instead. Web servers often have maximum time limits on web-based requests, so it’s likely that this will interrupt a large upgrade, plus the command-line upgrade process will provide more details on what the upgrade is doing that can help debug a failure.
If you do run this on a local machine, then yes, you’ll need to bring down a copy of the files directory in order to allow OJS to reconfigure it. After the upgrade, you’ll have to move the altered files directory back to your server along with the database etc.
The size of your database in itself isn’t a problem – we’ve run several large upgrades. However, the bigger the data set, the more likely you’ll have some weird outliers and integrity problems in your source database. If that’s the case, then start by finding out where the upgrade is failing by using the command-line tool.
Public Knowledge Project Team