Since it took me way too much time to figure this out, I'll write it down for future references.
I needed to move a git repository from one GitHub repository to another one that already had code, past PRs, etc. It wasn't a simple rename which would make GitHub redirect everything. It was adding a new history from one repository to another, while not getting rid of the past tags, releases.
When you squash a PR on GitHub by default it'll write the commit message (#1)
Where the number following the # character is the PR number. When viewing this message on GitHub it'll link to the PR page on the repo.
If you simply push that git repo to another github repository, it'll link to the wrong PR page.
To fix that you need to rename the #1 to a fully qualified PR link that GitHub understands.
It has the format: organization/repository#1
For that, I've used a tool called git-filter-repo.
git filter-repo --commit-callback '
message = commit.message
new_msg = re.sub(br"(#(\d*))", br"org/repo\1", message, flags=re.MULTILINE)
print(new_msg)
commit.message = new_msg
' --refs HEAD
On the target repository I created an orphan branch:
git checkout --orphan main
Pull the rewritten repository into main branch, and pushed to remote. That's it.