I've been plagued with a problem with my 12 string guitar for many years that even a very experienced luthier couldn't help me with. Because of the inherent design of most acoustic 12 string guitars, there is only one piece of bone for the saddle so on the bass string, 11th (lowest 'E'), the intonation is very poor, usually sharp. The repair was to bevel the saddle back to help but it didn't work very well. The only way to properly correct this was a very costly one which would probably void the lifetime warranty of the guitar. Replacing the bridge and saddle was not an option for me so I had to correct the problem without cutting or drilling anything.
What I did was lay a short cylindrical object behind the saddle (something hard like bone or metal) to increase the effective length of the string. The diameter of this object has to be large enough so the string will not touch the saddle anymore. After this, I adjusted the intonation almost perfectly by gradually filing away at one side of the cylinder and retrying it until the height just cleared the top of the saddle.