I have a custom field drop down box that I would like to rename - the values and field type are remaining exactly the same.
Will there be any knock on effects with past issues that the original field name used?
No, you'll be fine. The name of a field is just a display label for data that doesn't change in the background.
The issue you can run into when you rename custom fields is that users can define filters that say things like "... and customfield_dave > 12". If you rename customfield_dave to customfield_fred, their filter stops working.
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