Hum...
It is not a good thing to open a modded game with HW. Depending on whether you have the Moguri/Memoria mod, you should work like this:
== Without Moguri mod or Memoria Engine mod ==1) Make a copy of the game's (non-modded) folder. This copy (let's call it "FF9 - Copy") will always be used by Hades Workshop. "FF9 - Copy" is the moddable copy while "FF9" is the playable copy.
2) Thus, when using Hades Workshop, always select the file "FF9_Launcher.exe" in "FF9 - Copy".
3) When saving a mod, save it both as a .hws file and as a "Steam Mod" with options "Unity Archives" + "Compiled DLL". The .hws saves are very fast and relatively light in size, so don't restrain from saving often and possibly saving a new file each time if you want to be very cautious.
4) For installing and playing your mod, move the files from "FF9 - Copy/HadesWorkshopMod" (or whatever path you picked) into the related folder of "FF9".
5) When going back to modding, keep opening the non-modded version "FF9 - Copy" and then use "Open Mod" and select your .hws file.
HW *should* be able to open modded games as well but since there are so many things that can happen (like what seems to happen to you), I don't guarantee it to work. Besides, there are other problems if you work that way (the program can't "remember" what has been modded and what has not been changed, from a session to another). The progression bar only shows up during the loading of the game's datas, not the modifications contained in .hws (those are very fast to import as well), so if the program crashes during this progression bar, you can be sure that you open modded game files and the modifications are somehow problematic.
Crashing during the loading of enemies, it can pretty much only relate to the archives p0data2.bin or p0data7.bin (and to a lesser extent, resources.assets). I would urge you to use .hws files instead of modding on top of modded games everytime, but what you can do if you don't have any .hws and don't want to do everything again, it's replacing the problematic archive with the non-modded game's archive (test first p0data2.bin and then p0data7.bin if it still crashes in HW), then open every panel that you have ever modded, then go to "Tools -> Mod Manager" and check all the parts that you ever modded (it is better to tick more than necessary rather than fewer). Then "File -> Save Mod" will generate a .hws containing all the data sections that you have ticked.
You say that the problematic change was a script change "InitObject( 1, 130 )", in which case the problematic file is the p0data7.bin containing all the scripts. But that seems rather suspicious to me and I expect the problematic file to be p0data2.bin instead, containing the non-script datas of enemies. You'll loose your changes in one of these data types in the process.
Then switch to the workflow I described above, or better yet...
== With the Moguri mod or Memoria Engine mod ==1) No need for making a copy of the game here. In HW, always open the Memoria-modded game (Moguri includes Memoria).
2) Upon opening it, HW should prompt about using the vanilla "Assembly-CSharp.bak" or something like that; this is because Memoria makes a backup of a non-modded DLL and HW can use that backup. If it really finds no usable backup, you'll have to get one yourself by desinstalling Memoria, then copy the "x64/FF9_Data/Managed/Assembly-CSharp.dll" to a safe place, then re-install Memoria, then put the copied DLL next to HadesWorkshop.exe with the name "Assembly-CSharp_Vanilla.dll". Most of the time, though, this step works just fine without you needing to do anything.
3) Do whatever modification you want, and always save them both as a .hws ("File -> Save Mod") and as a Memoria mod ("File -> Save Steam Mod" with the options "Raw assets" + "Spreadsheets (Memoria)").
4) Enabling/disabling your mod is done by adding/removing your mod folder's name in the file "Memoria.ini" (sections "[Mod]", field "FolderNames", having something like the following: FolderNames = "HadesWorkshopMod", "MoguriFiles").
5) When you want to continue modding with HW, still open the same Memoria-modded FF9_Launcher.exe and then "File -> Open Mod" and select your .hws.
I don't accept donations. Here is why:
No, I don't have a patreon and I don't plan on receiving donations for my work in modding. In my opinion, everyone should earn a revenue high enough to live a decent life and possibly work toward their passions. I see donations somehow as a wooden leg trying to compensate for the lack of institutional will toward the rewarding of passion works and securing a decent life for everyone.
Since I am not in need myself and can afford to not use that wooden leg, I prefer not to and hope for a more satisfying framework.