If the fretted notes have grown sharp, then it means the break-over point on the saddle and the 12th fret are closer together than they used to be. It could be the neck pulling into the body a bit or the top torquing towards the neck (string tension works to fold the nut and saddle towards each other). It's also possible, especially if it has a tall saddle, that the saddle has begun to distort or lean forward, as string tension will work to do that, too. Check neck relief -- flattening it out, if there's room, will increase the scale length slightly, and might correct intonation a little. Eyeball the saddle. Try humidifying it a bit -- that might swell things back up if it's collapsed in on itself a bit. Barring that and, if it still plays well, you might look to rework the saddle or have a new one cut that's ramped towards its back edge, rather than crowned in the middle.