AFAICS, the problem is that Travis fetches a “merge preview” commit autogenerated by Github, +refs/pull/<PR#>/merge.
Which is regenerated by Github whenever the PR branch or the base branch changes.
This is a legitimate bug – but I don’t know whether it’s possible to get this commit any other way that would be protected from this effect.
Since you are an enterprise customer, you can report this bug directly to Enterprise support at enterprise@travis-ci.com and refer to this topic.