According to wikipedia, Ys: The Ark of Napishtim was released on PC in 2003. And an English translation (fan patch) has been out for years too. So it's probably just a repackaging of that.
XSEED has been quite diligent in the sense that they've done extensive work on the previous Falcom games they've released. Not only have they updated them to support modern resolutions, they've even ported the content that subsequent console/handheld re-releases featured. So at least so far, they haven't been just repackaging already existing releases.
That said, in Ys VI's case, there isn't all that much that could really be added from the PS2/PSP versions, since the additions were either of questionable value or actually made the game worse. Not to mention that it might not even be possible for XSEED to include any of it, since those versions were done by Konami rather than Falcom.
So aside from tweaking the game to work with modern resolutions as well as licensing and editing the fan translation (though I suppose they could opt to make their own translation), it is indeed likely that Ys VI will be a relatively straightforward re-release.