That's not really a question we can answer, it's a bit too vague.
You might mean "which jar/class/vm/etc files define how a custom field type works", or "when I add a custom field and name it Fred, where does that get stored?". In the first case, you'll need to tell us what you're looking for in more detail. In the second case, the answer is "there is no file, it's in the database".
Ok, you don't mean "files" then. The definition of a custom field is held in the database, and you'll need to amend that directly.
You could render your Jira completely unusable if you get any SQL wrong, and I certainly wouldn't try to delete a custom field with SQL.
What I would do is
Note that steps 1 and 2 really are mandatory. Never use SQL on a running Jira, and never run SQL against Jira without a backup...
That will make the cogs work, won't lose you any data and will let you continue working with the field (including deleting it if you're sure you don't want it any more).
From memory, your SQL needs to amend the table "customfield"
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