Ideally you would mix it in as it can take a while for the lime to work its way down if you just sprinkle it on top. I would be hesitant to remove the seedling just to redo the soil mix unless you're going to move it in to a larger pot while you've got it out. How old is it? My seedlings had elevated pH levels for just under a week and were fine after I got it under control. If it's a week or so old I'd say go ahead and transplant it to a larger pot while you're at it.
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