Different game features can affect a target at the same time. But when two or more game features have the same name, only the effects of one of them—the most potent one—apply while the durations of the effects overlap. […]
So with overlapping things, one instance will be “active” (will have effects) and the other will be “inactive” (won’t have effects). That said, I think my question will make more sense with examples:
The Fire Elemental’s Fire Form trait:
[…] The first time it enters a creature’s space on a turn, that creature takes 5 (1d10) fire damage and catches fire; until someone takes an action to douse the fire, the creature takes 5 (1d10) fire damage at the start of each of its turns.
If a creature is under the effects of multiple instances of Fire Form, and somebody uses their action to douse the fire, are both instances removed or only one?
The booming blade spell:
[…] If the target willingly moves before then, it immediately takes 1d8 thunder damage, and the spell ends. […]
If a creature is under the effects of multiple instances of booming blade, and they move, are both instances removed or only one?
The hold monster spell:
[…] At the end of each of its turns, the target can make another Wisdom saving throw. On a success, the spell ends on the target. […]
If a creature is under the effects of multiple instances of hold monster, and they succeed on a save, are both instances removed or only one?
Can an “inactive” effect end when its end-condition is met, letting them end simultaneously or do these sorts of things always end one at a time? Or perhaps something in-between?
There is also the following related question; an answer there supports that if you are grappled by multiple creatures and you make a check to remove a grapple, you only remove one of the grapples. It’s not perfectly analogous but it is somewhat similar: