When saving a temporary or user patch, the tool should reload the patch on the background before saving and compare it to the data that is about to be saved. This to ensure that the correct patch data is saved.

If the patch data has changed, show a confirmation dialog asking which version to save. Though it may be hard for the user to make an informed decision. Perhaps save both, so that the user can go back and try them? Cancel should also be offered as an option, so the user can chicken out :).