Merging back from master but keeping a subtree

I have a long lived branch that changes a directory and its
subdirectory, ie. 
 top/middle/mydirectory

Now I want to merge in an updated remoterepo/master and keep everything from that master, except for mydirectory and its subdirectory, where I would like to keep everything from my branch.

I tried a regular merge, and used
 git checkout --ours
 git add
and 
 git checkout --theirs
 git add
as appropriate on all conflicts.

But the result didn't build, and the build errors don't make much sense, so I think they are caused by "successful" merges giving bad results.

Is there a better way to do this?

Would it be possible to unstage the already staged files and apply the "checkout --ours" and "checkout --theirs", and then git add on the checked out files?

Even that would be clumsy... I would have preferred something like
 git checkout --theirs top
 git checkout --ours top/middle/mydirectory
 git add-only-those-modified-wrt-my-branch

Thanks!

- Steinar