It will make a difference in the taste whether you add it to the beginning of the ferment, or at the end. If you want to retain more of the flavoring you'd add it to the end, in a secondary or tertiary.
That's not to say it will taste awful, just that you'll change the cherry flavor letting it be fermented out.
If you have the means, you could try splitting your batch in half, doing one have with some cherry added, and half at the end and see which one you prefer.
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