If there was a way, we would automatically adjust the project when it was opened. Unfortunately there's no way to do it automatically, each flip has to be considered manually and an alternative chosen. 🙁 The old flip worked in a somewhat strange way
it always used the world axes to flip. Depending on your bone setup, using negative scale to flip may not result in the same flip. I wish I had a better answer for you! We didn't make the change lightly, but we had to make it to enable proper scaling, which is very powerful. Hopefully you find a couple hours of fixing up projects worth it for the latest version of Spine, if not maybe it's better to complete your project and use the latest on the next project.
