You'll get conflicts if you pull changes from the original repo any time the deleted files have upstream changes. After you record a merge resolution (presumably by deleting them again) you won't get conflicts until the next time those files change upstream.
If you submit a pull request part of its changes will be deleting the files from the original repo.
OTOH if you delete the files you can always undo that later with git restore --source upstream/main <deleted file paths>. You can restore them in a branch only if you do want to submit a pull request, but leave the files deleted in your own main branch.