We're currently using the pathauto "persist" patch from #195:
https://www.drupal.org/node/936222#comment-8770805
But there is a new one (made in response to Dave Reid's request) on comment #213:
https://www.drupal.org/node/936222#comment-9385937
It appears that this patch has gotten lots of testing and RTBC+1 action! So, it'd be great to switch to it and help add our RTBC+1 love as well. :-)
Unfortunately, there are always challenges with updating this patch! We'll need to have our own "patch to patch" hook_update_N()
function and do lots of upgrade testing in general. But it's worth the effort, especially if we can help move this closer to being committed.