I think there is no automatic way to merge different instances into one.
Probably export/import of submissions is the only option (with all the data loss that implies).
Import/export is one of the big items on PKP’s roadmap, but it will be a long road:
Why not keep them split and build the magazine journal in the front of them with a different tool?
This is a 10 years old drupal (I mean, look&feel need to be updated) but the idea is still valid:
https://revistes.uab.cat/web/en
Cheers,
m.