Ah, thanks for the info.
Just nearly 100%ed this game (100% map, 100% souls except Hell fire, all final forms of all weapon types). I decided to add in Soul Vessels (like the Doppleganger one in the Garden) for the three bosses whose Souls you have to sacrifice in order to synthesize certain weapons (Gergoth, Death and Abaddon). I noticed that if you already have the souls, the Vessels won't appear, until you lose the souls by using them for synthesis, so I placed them before the boss chambers.
My question is, will obtaining the Boss Souls from these Vessels before fighting the respective bosses prevent the bosses from dropping their Souls?
Nope, the disappearing early thing is specific to soul candles. Unlike most items soul candles don't have pickup flags to keep track of whether you got them or not, so they just check if you own the soul inside them or not.
Bosses on the other hand always drop their soul when killed, and the boss itself doesn't disappear until its boss death flag is set.
Another question I have is, I want to make the Alucard Sword an obtainable item. I was wondering about the pickup 'flags'. Does every item have its own unique flag? What flag should I give a newly placed pickup?
The pickup flags need to be unique throughout the whole game. If you give two pickups the same flag, then picking up one will make the other disappear too.
Fun fact: The developers actually made this mistake in PoR. They gave two MP max ups the same pickup flag, so it's actually impossible to get all MP max ups in one playthrough. They did the same for a potion + an antivenom, though those are less important than MP max ups.
For what flag you should give the pickup, flags 00-7F are valid in DoS, but most of those are used. Flags 7A through 7F I'm pretty confident aren't used anywhere.
There are a few more besides those that aren't used anywhere I know about, but because their numbers aren't at the end they seem like they may be used somewhere (or were used at one point in development at least): 01, 09, 14, 1B, 1C, 1D, 24, 4E, 52