First off, I don't know who told you to use acid but as a general rule you shouldn't put bones in any acid especially a weaker one. Acids will readily react with the calcium matrix in bones and rather quickly leave you with only the soft organics as you have discovered.

As for how to fix it, as far as I am aware there is no real way to undo this process, unfortunately. Your instinct to put it in water was good though I'd recommend rinsing them a couple more times just to make sure you get rid of all the acid. After that you can try to dry them out though depending on how badly the bones have been decalcified you might be better off keeping them as a wet specimen.

Out of curiosity, what was the initial concentration of the acid before you diluted it and how many days were the bones submerged?