To add a bit more information:
github.event.workflow_run.pull_requests returns nothing when a PR is created from a fork, but returns everything you would expect when a PR is made internally to the repo. Unfortunately, I don't think there is really anything that can be done at the moment. This is either a bug in GitHub Actions or unsupported activity.
I have found a workaround using the issues search API. I will post a PR with my updates in a little while.

Seeing as your PR changes to search API and this commit seems to change away from search API 99348f4
-perhaps it's enough to revert it.
Could you please try the old version of the script and see if that works just as well as in your PR?

Forgot to post the actual old version of the script that I mention. Here it is. https://github.com/oprypin/nightly.link/blob/4e83d1452dd1bf350ebe1a3910e395e6cf447fdf/.github/workflows/pr-comment.yml

I tried the old version in my repo https://github.com/ooshlablu/performous
It failed with the error: No matching pull request found

I certainly am having this problem. Can it have anything to do with the recent update of actions/github-script to v6?

You tell me ¯\_(ツ)_/¯
Just try the version before that https://github.com/oprypin/nightly.link/blob/4e83d1452dd1bf350ebe1a3910e395e6cf447fdf/.github/workflows/pr-comment.yml

Here's the version you suggest, working fine with a PR:

https://github.com/drud/junk-test-pr-comment/pull/2

OK so in the meantime you can simply use that if it works better. There's no requirement that the script currently merged in the main branch here needs to be used, there are no permanent references to it.
I don't know when I'll get around to considering this issue.

In the test repo I did try out the new/current version just to verify; it fails as described here. But the old version, https://github.com/oprypin/nightly.link/blob/4e83d1452dd1bf350ebe1a3910e395e6cf447fdf/.github/workflows/pr-comment.yml works OK.

For me, just reverting to https://github.com/oprypin/nightly.link/blob/4e83d1452dd1bf350ebe1a3910e395e6cf447fdf/.github/workflows/pr-comment.yml did not work, I got:

…
TypeError: Cannot read properties of undefined (reading 'list')
Error: Unhandled error: TypeError: Cannot read properties of undefined (reading 'list')
    at eval (eval at callAsyncFunction (/home/runner/work/_actions/actions/github-script/v6/dist/index.js:15143:16), <anonymous>:8:36)
    at eval (eval at callAsyncFunction (/home/runner/work/_actions/actions/github-script/v6/dist/index.js:15143:16), <anonymous>:16:3)
    at callAsyncFunction (/home/runner/work/_actions/actions/github-script/v6/dist/index.js:15144:12)
    at main (/home/runner/work/_actions/actions/github-script/v6/dist/index.js:15236:26)
    at /home/runner/work/_actions/actions/github-script/v6/dist/index.js:15217:1
    at /home/runner/work/_actions/actions/github-script/v6/dist/index.js:15268:3
    at Object.<anonymous> (/home/runner/work/_actions/actions/github-script/v6/dist/index.js:15271:12)
    at Module._compile (node:internal/modules/cjs/loader:1105:14)
    at Object.Module._extensions..js (node:internal/modules/cjs/loader:1159:10)
    at Module.load (node:internal/modules/cjs/loader:981:32)

did anyone find a stable solution that works with the current API?

This might be a working option: https://github.com/HarbourMasters/Shipwright/blob/071a2d0418d6fb7464a1ddccd2b647683da38eff/.github/workflows/pr-artifacts.yml

This one works for me now: https://github.com/AKSW/submission.d2r2.aksw.org/blob/680c23f975f51f06e6a4b7e212b56abfeca8f800/.github/workflows/pr-comment.yml