If you've met more than one firekeeper, you can kill some of them. Sure, it's cruel but it's a very in-universe solution.

How many have you used? I believe you can upgrade the flask a max of 6 times in one run, but it's very unlikely someone in a blind playthrough would find more than 3 or maybe 4 of them. If you've used 3 or fewer, you can look up how to get the remaining ones and just be content with the fact that you're on a normal pace. Reminder that one fire keeper must be alive to upgrade your flask so don't go too wild. Also losing any fire keeper kills their bonfire permanently, so be prepared for that.

Ultimately, losing the flask upgrades is a bummer, but it is not as devastating as I'm sure it feels right now. You can still do this.

(I don't know of a way to restore them or upgrade the flask without them but I got this helps anyway)

You can use Cheat Engine to alter the ID of one item to another. So you can change a few arrows or a broken sword hilt into a Fire Keeper soul.

If you're on console, there's no way to fix it, but you can play around it. Get the remaining ones you can, only level Vitality enough to heal about 80% with one Estus chug, then put the rest of your points in Endurance, which will increase your carry weight, allowing you to wear stronger armor. Next, find a good shield and adjust to a block-heavy play style.

Or, if you want to challenge yourself, do Vitality per above, but only put enough points into Endurance for you to roll two or three times, then put most of your points into Dex, Strength, Int, or Faith, wear no armor, dodge everything, and be a glass cannon.

You get another go at them in NG+, which you need to go into to get the full +7 bonus anyway.