I've heard about negotiating a treaty between the NCR and BoS. Is it true?

Question

Can I do this and can I still do it if I have already overthrown the 1st elder?

Answer 1

Yes, it's possible, but only with Elder McNamara, not with Elder Hardin.

Answer 2

You can make a treaty with Elder McNamara, but not with Elder Hardin.

This is done during the NCR main quest For the Republic, Part 2.

From Nukapedia:

If the player has completed Still in the Dark, stayed on good terms with the Brotherhood, and McNamara remains Elder, a truce can be signed between the Brotherhood and the NCR. Go to McNamara and tell him the NCR wants them destroyed, he will offer a truce. Return to Colonel Moore and speak to her about the offered truce. Doing so will complete the quest and begin You'll Know It When It Happens, but will earn the player minor infamy with the NCR. This method should work if the player has completed all main BoS quests as well. Note: If the player chooses to help usurp McNamara, they will be unable to broker a treaty.