Be careful with the Beyond Compare comparison (or Araxis Merge, or any other comparing software you use), especially if you're not comfortable with it. I won't make it sound hard, because I'm sure it isn't (I've only done it once and I can't recall the outcome offhand), but still be cautious.
Natch makes a good point in doing a backup before uploading the newly-upgraded files. But I'd recommend going even one step further and doing this on a testboard. Create a copy of your existing forum and db and upload the newly-upgraded files there first. If all works, then repeat the process on your existing forum. If not, you have a good chance of ironing out any kinks without harming your original board.
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