I upgraded to V3 today from V2. My old settings were *supposed* to be available in an "old" folder that I could then import. This folder apparently was not created and my old settings were not saved in the XML file. It appears the upgrade completly overwrote the old install.
And if you manually save settings from v2 there's no way to import them in V3 later.
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We dropped the ability to upgrade from 2.0 about a year after 3.0 came out as everyone should have upgraded by then due to security issues, etc (2.x has been dead for a year and a half now) Looks like we forgot to remove the note from the support page though it was removed from the instructions and release announcements. I've removed the note from the support page.
Sadly, this was a limitation of FileZilla itself and caused much uproar when it happened. FileZilla itself is supposed to warn you of the issue, but it looks like it now just resets the settings on you (it would appear that they don't expect anyone to be using 2.x anymore either). We used that backup copy workaround to make it easier on some folks when upgrading. I'm actually surprised anybody is still using 2.x this late in the game. I'll adjust the launcher to handle it properly in the next release on the off chance it happens again.
Thankfully, you can grab the copy from your most recent backup and then import it into FileZilla 3.
Sometimes, the impossible can become possible, if you're awesome!