Communication.
Tools can't solve this for you, unless the specific tool is your email or IM client.
It's the same as if you were making any other major change in a shared project -- you need to be able to tell your coworkers/collaborators "hey, hands off for a couple of hours, I have a big change to the FooBar module coming in".
Alternately, if you're going to be making a change so major that it has the potential to cause huge merge conflicts with the work of 10 other people, run the change by them beforehand. Have a code review. Ask for architectural input. Then, when you're as close to consensus as you're likely to get, take that virtual lock on the section of the repository you need, check in your changes, and send out an all-clear.
It's not a perfect solution, but it's as close as you'll get. Lots of source control systems support explicit locks on sections of the source base, but I've never really seen those lead to good results in these areas. It's a social problem, and you only really need to resort to technical solutions if you can't trust the people you're working with.