No. it doesn't. It just applies the base persistent damage as an effect.
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Thank you for all your responses Trenloe. This is actually where I explained myself badly due to my English proficiency being a bit rusty.
The fire giant has the effect immune and takes no damage by the roll, as it should. What I meant to say was that the persistent damage effect is still applied, even though it has no possible effect. I meant that it could check before applying or rolling to forgo the whole roll.
And I just thought this, because there are the options to hide or show the GM rolls as well as fudging them/doing a manual entry. I just believed that it might be another option I was missing, to make it appear as if the enemy is still fighting the persitent damage it is not really affected by. Maybe for those parties that never try to figure the enemy out with a recall knowledge check. Hopefully I make a bit more sense now.
And this one is working perfectly. I don't even know why I missed this option while trying the damage type. Was this listed in the Pathfinder 2e Effects Wiki entry and I just overlooked it again? What most likely lead to me missing it is he fact that I misinterpreted how the punctuation mark works. I thought it would denote multiple types of damage for the same damage roll, like "1d8 slashing, magic".
And one last thing: I tried to check the Ruleset Bug Spreadsheet first, but couldn't find it in there. If the attack were to hit a second time in the same round or next round, after the enemy failed the flat check, it will apply the persistent damage effect a second time. Now the enemy will roll the 1d6 and the flat check twice, while applying both instances of the 1d6 damage.
Thanks again for your help and hard work.
one thing to watch for when applying persistent damage from weapons is that it doesn't stack but Fantasy Grounds doesn't yet notice this so if you don't keep an eye on it you can easily end up with multiple bleed effects on a PC or NPC