Labels exist while there are issues labelled with them.
Therefore, you may search for issues having the label you would like to remove and perform a bulk edit operation on all of them to remove the label.
As soon as no issues were using said label, the label would stop being suggested for autocompletion.
Hope it helps.
I am not sure what the question is
>I have created an open ended custom field as label.
What do you mean by "open ended custom field"? Is this a text field in which people can type as much as they like? A short text field? An actual label field?
This matters because the method of de-duplicating data in a field. If you really do mean just "I created a label field", then @Ignacio Pulgar 's answer is right - use bulk-edit, searching for each label you want rid of, and replacing it with a better one. If it's some other type of field, we'll need to explore that more.
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