Can I use “soon” in the following manner?
I had some garlic at lunch and smelled bad. But thankfully, the smell has soon worn off, and I smell fine now.
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Not quite, but we can adjust the sentence slightly. Given that the person who ate the garlic is currently smelling fine, we should indicate that the smell wore off (quickly) - emphasizing that this process happened and ended in the past.
In the present perfect construction, we are limited in what adverbs of time we may use. 'Soon' is not one of them, but it can be used with a past simple construction, which is what I would suggest to use here.
Let's change it from the present perfect tense:
the smell has [...] worn off
to the past simple tense:
the smell [...] wore off
Your sentence would then read like this:
But thankfully, the smell soon wore off, and I smell fine now.