Once a word is in the OED it stays there forever.
What the OED says is "Used as a deliberate antonym of ‘inept’: adroit, appropriate, effective."
Some words that have no current positive sense (like 'couth') did once have a meaning independent of their negative counterpart (in that case, 'uncouth'). OED's findings don't suggest this was ever the case with 'ept'. (OED is a subscription-only service, so no link.)