Why would you want to delete it? I would assume that there is some way on the login page to do it. If not try going into the game and look and see if it is on the main menu there.
To make sure, I just made an online saving slot with a new character, played a bit and then deleted it, which worked fine for me. You are logged into the website for both occasions are you? Both the website itself and the online game saving? It should work fine then. =)
Besides, you can restart the game, by making a new online saving slot and start from there. The game and the website should follow that saving slot and grant you the Quests as normal when they are achieved. =)
Strike my last comment, now I need to reset my game, because I can't buy the armor piece I need, and the mission to get it is lock because I've already used it.
Hey! Hands of War 3 developer here. I tried to recreate the problem you're having, but I've had no luck. There must have been something corrupt with the data that was saved to your account in that save file. I would first make sure that you're using the latest Flash Player - using older versions causes unexpected things to occur.
There are three save slots for both online and local saving. Can you just use one of the other save slots to restart your game?