You'll be presented with all your commits, you can choose to exclude some from the rebase (useful if you had to update something specifically because it gets updated between every PR/build), then commit to the rebase. It will then proceed to replay each commit you made, just like a repeated version of your stash/unstash process, on top of the new top of the master branch. Your working branch is now contains all the changes you made, but instead of working off your PR commit, it's like you were working off of the finished PR commit.
If you want to make sure that your git history maintains the old branch for sentimental reasons (or you want to try out removing some commits and desire an easy way to rollback if you get lost), just make a branch off of your working branch before the rebase. That branch will be identical to the branch you were working on, before the rebase.
A---B---C topic
/
PR Branch P---R---S
\
O---L---D---E master
(where commit D and E are produced as part of the PR, say, the merge commit and a version number crank or something)(checked out topic) git rebase master
PR Branch P---R---S A---B---C topic
\ /
O---L---D---E master
magic