I assume you're going to your Admin panel and then clicking Destination, finding the one you want to delete, clicking Edit and then clicking Delete at the bottom?
There's a faster/easier way to do it that has never generated an error or warning or anything for me. In your Admin panel, if you hover over "Destination Merging" it says "Use this feature to delete Extra Destinations". It's quick and painless, as long as you're sure you don't want those destinations anymore.
As far as other parts of the site using the destinations, only thing I can think of is DKP standings.
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Ieyasu - Organizer,
Ex Cineribus