I hope I understand the task correctly.

The test phrase should be placed in double square brackets.

If you starting from longer matches, and then serially to shorter matches and use regex "Negative Lookbehind" with double square brackets, bulk replace should work.

(?<!\[\[)

It will only replace phrase without double square brackets in front. For higher accuracy, it can also be additionally tested below.

Please let me know if i have understood your problem correctly and if my suggestion helps

file-result