I think the topic batch updates needs an improvement.
There’s a technique to update the application after a batch update mentioned by Apple:
(See Section »Updating Your Application After Execution«)
This is really useful and should be implemented per default in my opinion.
I’ve ran into a strange bug myself due to this and Apples solution works just perfect to tackle this.
Apples code example is a bit dated but Xcode is very helpful implementing this.