Upgrading Drupal, or any application for that matter, is often much harder than performing an installation from scratch. Two major hurtles come to mind.
(1) Compatibility. Will all your stuff still work with the new version?
When Microsoft releases a new version of their Office suite, for example, you want to know that *all* your Word documents created by previous versions can still be opened.
Drupal, unfortunately, doesn't make things that convenient. In the cosmic balance between the software pragmatists and the software idealists, the Drupal team, unlike Microsoft, fights for the idealists. Any time they release a new "major" version (that is, 5.x to 6.0, for example), they pretty much guarantee that all existing custom themes or modules will *not* work. This is because they are very much willing to throw away a large part of the codebase if they think there's a better way of doing something.
These compatibility issues, however, are not an issue with "minor" upgrades (such moving from 5.4 to 5.5). This is because minor upgrades usually deal with security fixes and implementation details that your custom modules and themes don't care much about. Luckily, the upgrade I wanted to perform, 6.1 to 6.2, was a minor upgrade, so I knew with a high degree of confidence that all my custom themes and modules would still work (and they do).
(2) Data preservation. Will any of your data be lost in the upgrade process?
Of course, you want this answer to be a resounding "NO WAY!". For example, if you upgrade to a new version of Firefox, you don't want to load up your new version, only to find that all your bookmarks are gone.
I find it helpful to maintain a list of all of these differences. That way, whenever I have to upgrade, I know exactly what files to put back into the new version to keep my site running smoothly.
Now that you've got an overview of what to expect from your Drupal upgrade, you might want to do some reading on the Drupal website for more of the technical details. Good luck!
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