Sorry you are having trouble. As you found, the way scaling and flipping works changed in v3, described here:
Blog: Spine 3.0.00 released
This isn't something Spine can fix automatically because the way scaling and flipping used to work is not the same as scaling a bone using -1. Unfortunately the only way to fix it is to rework the animations manually. 🙁
Note this is the only time we have ever made such a large breaking change. I know it is very inconvenient for old projects, but we felt it had to be done because the new way is so much better.
Can continue discussion here:
官方可否支持解决一下WARNING: Removed timeline (flip Y no longer suppor