This is definitely not the best method but this is something that worked for me
- clone the Repo (from where you want the subdirectory)
git clone --no-hardlinks repo2
- Select the folder you want to keep
cd repo2
git filter-branch --subdirectory-filter path/to/subfolder HEAD -- --all
- Remove everything else
git reset --hard
git gc --aggressive
git prune
git remote rm origin
- Add the Repo where you want this subdirectory in and clone it
git remote add origin repo1
git pull origin master --allow-unrelated-histories
- Commit and Push
git add --all -A
git commit -m "whatever"
git push origin master