Hi @Sleipnir,
The native XML import/export format is not intended to be stable between releases; in particular with OJS 3.2 we introduced a versioning feature allowing each submission to have multiple versions (in order to track and expose revisions to readers, for example). I would suggest comparing the schema files (plugins/importexport/native/native.xsd and lib/pkp/plugins/importexport/native/pkp-native.xsd) to see what has changed since 3.1.2.
Regards,
Alec Smecher
Public Knowledge Project Team