But the trophy data is verified through PSN once uploaded; I don't see why using a game save generated on a different console would have any effect on that.
Most games that don't want "unlocks" transferred use locked game saves that can't be copied, but admittedly I haven't tested all this out.
I'm currently in the same situation; my primary PS3 died about a week ago and I was only able to copy saves and make an archive after temporarily resurrecting it, but I was unable to get a successful complete console to console data transfer and have since reformatted the drive.
The archive created on one console did transfer some data to the other console, contrary to what I thought would happen, as I was under the impression that archives were completely locked to the console on which they were created.
Not true.
However, locked game saves and PSN content (purchases, DLC, etc.) do not transfer (no surprise there). Non DRM video, photos and music content will also transfer in addition to non-locked game saves. Better than nothing.
While I can't verify FFXIII (I do have a game in progress with archived game saves to test it out), I can say that other games will allow you to "continue" unlocking trophies on a previous game save, even if it wasn't created on the current console you are using.
