There has been no update to the factory presets for the FX3.
The FM9 factory presets are not the same as the FX3 presets in a number of cases; The FM9, even the Mk II Turbo, is still about half the power of the FX3 Mk I so some presets will overwhelm the FM9. The
factory presets page in the Wiki helps explain when they diverge. You can load the FM9 factory presets into the FX3 but you'll be missing the originals in memory at that point.
I opened the first factory preset on the FX3, then used Edit's "Set in Multiple Presets" feature (
<shift>
+
<right-click>
) on a "safe" parameter, I used the Level in the In 1 block but YMMV, and told Edit to set all the factory presets to that value. Edit stepped through all the selected presets, loaded then saved them, with the Level "updated" to its original value. That load step will automatically update the Amp block's parameters so they're "fresh" and they'll then be saved as part of the process.
At that point you won't need to step through them all and manually save them.