Oh this makes sense bro, I've been aware of the specific portion of Jonathan's leg being a result of engine reuse; but I still hold my original opinon for about 40% of total rate in my mind, for some reason. Though there did exist lots of leftovers from previous games, the Belmont sub weapon case alone still could be anything before an estimate answer shows up.
OK let me put it another way. You know the files you found in /sc2/f_ub01.dat, /sc2/f_ub03.dat, /sc2/f_ub13.dat, /sc2/f_ub14.dat in Order of Ecclesia? Open Portrait on the editor and look for the same exact files.
Here's /sc2/f_ub01.dat:
Here's /sc2/f_ub03.dat:
Here's /sc2/f_ub13.dat:
Here's /sc2/f_ub14.dat:
So you see, not only they are the same exact graphics, but they're also on the
same exact files. And now, considering they're grouped more or less on Dawn of Sorrow space, I'd wager that they're actually Julius Belmont's leftovers, not Jonathan's. If you open Dawn of Sorrow and just remove the 2 from the sc, the same graphics surface on the same files again. The fact that they are in the "sc" folder in Dawn, but on the "sc2" folder in Portrait and Ecclesia merely proves that they got more organized as the engine got more robust with newer games. And, sure enough, Julius has exactly the same subweapons present on these files (Cross, Holy Water, Axe, Grand Cross).
Please, don't take this as me presuming to "speak for the developers", if that's what I come off as. But I
think these files on Order of Ecclesia do not mean they were "developing one thing first, then scrapped everything and changed their ideas later". They appearing on all three DS games with the same graphics and same files, are pretty good evidence that they are simply leftovers, left there for convenience (and the funny thing is that Soma appears on Portrait data, and both Soma AND Jonathan appear on Ecclesia data, as if the devs were growing lazier with every new game heh).
And YES, it's awesome to see what this tool can do. I've already had quite a bit of fun with it lol