Toilet leaking at flush pipe.

I am having a problem with this toilet that the original owners of this bungalow must of had before, given that this toilet has always been there. I originally investigated a leak coming from the L shaped flush pipe where it goes into the toilet at the bottom. I noticed it when I was taking the toilet out in order to fit tiles, great I thought an easy enough job wondering why whoever originally installed this toilet had used silicone to fill in between where the pipe fits the internal pan connector so I thought well this has been leaking a good while, evident by the water marks on the boarded floor. When I investigated I found the the internal hole where the pan connector goes that the toilet had a manufacturing defect in that hole. it has a lip which prevents the pan connector from sitting true in that hole which led to it leaking, but at the time I didn't have a ceramic file so I put it back together and I to used silicone thinking on the flush it would not leak, well two years later it has done exactly that and quite honestly I am scared to go near it, having done all the work once I really never thought I would have to do it again, but I do. The first time round I put a new soil pipe with a bath connect, and I am scared of unsettling this lot as at the time of fitting all the floor was up and there were numerous plumbing mistakes evident. Should I drag it all to bits and lift the tiles at the back to get at the effluent pipe or should I just re-silicone the flush pipe back in? I feel sure that if I take out this lip inside the toilet flush hole with a ceramic file the pan connector just might fit and sit correctly and that would be job done. Help please.

Don't use silicone if you go the easy route. Use a polymer like CT1 or Stixall. It sticks to wet surfaces and sticks better than silicone and will last.

As for your question.

Up to you if you want to rip it out and start again fixing the issues. Probably what i would do