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)