Cooling Leak

1989 Daihatsu Charade 130000 Miles. It is a 1.3 4 cyl 5 speed EFi hatchback. Problem is engine wouldnt start, took it in and was told it needed the head gasket replaced because it was leaking water into 2 cylinders, dont know why, head gasket had been replaced only 4000 miles before, only thing was I left the car garaged for 12 months without driving it, when I started it again it ran fine for a couple of days then wouldnt start. So I paid to have the engine pulled out, head machined and gasket replaced. When I went to get it back the mechanic said that he had to rerout or disconnect the heater because it was leaking water into the engine, I asked why it was leaking and he couldnt tell me, just said that I should sell the car asap because he found internal problems with the engine, then went on to tell me that he found a hole in the transmission casing that he had to plug with a cork and tried to convince me the hole was there when I brought it in! It wasnt, I always change my own oil, plugs etc. And I know there was no hole in the metal housing (I should mention im a qualified machinist, no worries servicing the basics but know jack about the insides of an engine, and there was no hole when I checked the fluid level in the transmission) The car has been running perfect for 18 months now, every now and then it idles a bit low but rarely so my question is why would he have to disconnect the heater, there was nothing wrong with it before or did he screw it up like he screwed up by somehow punching a half inch hole in the top of the transmission casing when he was working on the engine? Its a great second car, I dont want to sell it but if there is something wrong with it.