Remember, you are working with two repositories. One that is on your local computer, one that is on Github, (and third on JuliaLang/Julia).
It’s important to keep your local copy (the one on your computer synced) with the Julia master. This is done by following the instructions on Syncing a fork - GitHub Docs
Then, you can a) push your local copy, with all the changes you just pulled, to your github repository. Now that your local and remote are synced, you create a branch, work on a PR, then push your changes again to your github OR b) you realize that once you sync your local, there is no need to push the changes to your github right away. You can now create a branch, work on a PR, and THEN sync all of this to your GitHub repository, which will then allow you to submit your PR to Julia.
I occasionally make PR’s for corrections or clarifications to the documentation. This is relatively easy to do entirely on github without pulling the repo to my local drive. However, if a six-month interval passes between my documentation PR’s, then my branch on github is hopelessly out of date. So I do exactly as the OP suggested: delete my entire julia repository on github and start over.
I don´t have a black belt in git, so perhaps my advice is not very good. However, I found this tutorial on “GitHub Standard Fork & Pull Request Workflow” helpful. By the way, there are errors in the links in the contributing section at the julialang repo which this pr fixes, but it has been forgotten…