That happens to me a few times in the past, and now it's becoming more common as i do more volume automation and consider it.
There's nothing wrong with changing it's balance in the mix as the song evolves. I would even suggest rendering out a few clips of that sound and depending on how it fits in the mix, should have different settings.
The point is this, you have to make things fit and work. You gotta solve the problem as a sound engineer.
There's several ways to skin a cat, but this concept you're asking about is the beginning of the infinite nature of many concepts that lead to true self expression. It's way past the basics and fundamentals. Which is probably why it's not common.
Basically, make it sound good at the problem areas because it's part of the mix. It may require duplication, rendering, volume automation/settings, eq automation/settings, or not even have it in that spot.
I asked my music teacher about this sort of question, and he basically said "That's up to you man, it's taste." He couldn't give me any more "technical" advice because that's where your problem solving skills and taste as a producer/engineer start. That's where the real fun begins.