It's very uncommon for a company to handle its own ports. In fact, the only port I know of that was handled by the company who originally developed it is the Kingdom Hearts 1.5 HD ReMix collection.
Examples:
FFVII PC : Eidos
FFVIII PC: Eidos
Mass Effect for PS3: Edge of Reality
Dragon Age for PS3: Edge of Reality
The Sims 3 (PS3): Edge of Reality
etc etc.
It's not like upscaling a game to HD is a particularly taxing task, its just time consuming. It's all repetitive sutff: extract file, decompress texture, increase size (probably using fractals), blah. In all likelihood, they had a batch process set up to carry this out on every texture in the game at the click of a button, then just had a person go through it and see what ones needed to be redrawn afterward.
The only input needed from SE would have been if something had to be redesigned: i.e. the menus or Tidus. Remember how his hair lacked colour before? SE probably looked at it and went "that's not right, fix it, make it closer to the original" and so they shuffled off and did it. That's pretty much how porting works, except we know in this case SE actually had an involvement, whereas normally what happens is the publisher (which is not always the original developer, see Bioware (published by EA, decisions like this are not theirs)) just throws money at a random developer who's known for doing ports and tells them to get it done, throwing them a copy of the game and if they're lucky, some development stuff.