No, that will happen whenever you pull in the changes from them. You basically do a merge of their branch into your branch, which is really similar to making a PR to them (in the former case you integrate their changes into your repo, in the latter it’s vice versa). In both cases Git will observe two conflicting sets of changes (one branch modified what another branch removed)

If the themes change in the upstream, I think you’ll still end up with “both modified” type conflict, “modified by them and deleted by us”.