krammor The issue you describe is indeed reproducible, but not only that, there is data that is not exported even if the non-essential data is checked (for example, the stored selection group will be lost). Therefore, the first thing I would like to mention is that we recommend keeping the original Spine project.
However, it is quite possible to re-import and upgrade skeleton data, so I have created an issue ticket to include the order of the bones in the Weights view in the exported skeleton data in a future update: EsotericSoftware/spine-editor862
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