Hey paule32,
I don't mention if you're using trunk or stable, but I think I can deduce that you're using trunk.
In this case, that's the actual intended way of things to happen. When updating from trunk, or using trunk, you have to have the latest version of the code that is upstream.
Now, another thing that is worrying me is that you're changing stuff on the source branch and you wanna stop getting updates on it. That's not really a good path to take.
I don't really have a good solution for you to change the core code and not keep it updated.
Sure, there are some very messy ways to go around that by having a copy of the file you wanna change on the folder where your source lives, then cross your fingers that the compiler picks that first and doesn't complain too much about duplicate units...
Nonetheless... It's not a good practice.
BTW, what are you messing with? Maybe it's good enough to ask the core team to accept your changes... Who knows, right?
Cheers,
Gus