I don't know what respawn system you're using (or how you determine that something is a boss), so don't expect a detailed answer, but logically it would make sense to edit the system you have to either a) not apply to the boss (-es) and create a seperate system to respawn them or b) use different respawn timer within your already existing system depending on what "rank" of creature it applies to.
Have you tried any of that?
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Also, you already have a recent thread about a very similar issue:
[Trigger] - Respawn system
Why another one?