You change it.
Like adding in an additional POV, this isn't a task for the faint of heart. But it's not impossible.
First of all, why are you taking out this subplot and replacing it?
Hopefully, it's to make your story better. In my case the subplot was a means to an end, as cute as it was, it was the end result I needed, not the subplot itself. There were plenty of other things that could happen to get the outcome I needed. Hopefully, changing the subplot would even out the tone of the story.
What will you put in it's place?
I put a lot of thought into what would get me the results the story needed while still working within the framework of the story. Since my goal was to even out the tone of the story, I needed to keep that in mind while choosing subject matter. I also wanted to minimize changes that didn't make the story better/move it forward/etc.
For the most part I'm a pantser, and when I do outline, it's in a synopsis-like format. So the first thing I did was make an outline of each chapter, what scenes it contained, and what each scene was about. I highlighted all the scenes that focused on the subplot so I knew what to change. I also highlighted any little references within the text itself that were sprinkled about that would need changed so I could make sure to fix them. In the outline I also added what I was going to replace each scene with, so I wouldn't forget. It was vague, just a framework, and easily changeable, but it also served as a reminder so I knew what I meant to put there and wasn't trying to recall it weeks later.
Then, I got to work, using my outline to figure out where to insert the new scenes, going back and changing the things that no longer worked...and finding all those pesky highlighted sentences. It took a lot of time, not only to add in the new subplot, but to make all those little changes to ensure it worked. I had to catch all those little references, insert things here and there so the changes make sense, and most importantly, make sure the writing sounding the same, since these new parts were writing long after the original.
The thing that helped most with this was making sure I was organized. (Also, I did all these changes in a new version of the story so I still had the original version for reference.) This is what worked for me and for my story. For you it might be note cards or excel or a white board or rewriting the story from scratch. The most important thing is to not get discouraged--after all, you're doing what you need to do to make the story better.
While it took a long time to make the changes I needed to, and I had to edit it over and over to make sure it had the continuity it needed, it really did make the story better. And in the end, that's what matters most.