I have a solution, with a vb project and a window with some controls and a WebControl. I resized the window, saved, et voilà: the WebControl disappeared. I closed and restarted VS and it seems to be gone forever...
Go into the form designer file and remove all lines containing the webcontrol. This deletes the webcontrol so you can add a new one. Then name the new webcontrol with the same name as the old and everything should work fine