Does this imply that the two instances were on different versions and/or had different plugins installed? I think my expectation if I were doing a merge like this myself, would be that before anything else I should:
- Take backups from both
- Ensure that both are running the same version of Discourse
- Ensure that the target has all the plugins installed that the source does
- (Optional?) Ensure the source has all the plugins installed that the target does
- Take backups again