Can I restore my wiped out Religion in Civ 6?

I believe you have lost the religious war, friend.

You are correct about Great Prophets; there are indeed a limited quantity of them. In my 6-player game on Prince difficulty, there were 4 Great Prophets. I believe you are also correct in saying they are used strictly for founding a Religion. I did not notice any other options for that unit during my game.

As you have mentioned, buying units with faith corresponds to the dominant religion in that city. If you still have citizens following your religion, there may be some small hope for the pressure to bubble and your religion to become dominant again, but that is unlikely at best. Cities spread pressure based on how many followers are in that city; the dominant religion will almost always be emitting the most pressure. If you chose traits that increase pressure in some way, your religion might resurface. Otherwise, I believe it has been lost to the waves of time.

DISCLAIMER: This game is a new release, and this evidence is almost all anecdotal from gameplay experience.

You actually might still have a chance. Killing religious units reduces that religion in a radius by up to 250. So just declare war on who ever is the majority and run over all the missionaries and apostles with horseman.