From a systematic view, it’s just data cleaning. Regex replacement is one option.
A quick search for “regex” turns up plugins Regex Pipeline, Regex Replace, Paste transform, Auto replacer, Search and Replace Regex, and more. Some of those say they automatically run when pasting or with other defined rules.
A starter search string you can test to see if it catches all of your pasted citations:
/^\[(\[\d+\]\(.+\))\]$/
If that works, then the replacement string for that is: $1