Steps to reproduce:

Prepare the environment:

• Prepare two eZ Publish 5.3 installations, fully updated (5.3.5). One will be your source server, and the other will be the target server;
• Install eZ Content Staging 5.3 on both installations. More details here:

https://doc.ez.no/Extensions/eZ-Publish-extensions/eZ-Content-Staging/eZ-Content-Staging-LS-5.2.0

Reproduce the issue:

1. Source: create 6 articles e.g. Article 1, Article 2, etc;
2. Source: sync the resulting 6 events;
3. Source & target: create new content class (called it "13479" in my tests) with an attribute of type "layout" (please import the attached "13479-1.0-1.ezpkg" package);
4. Source & target: configure /ezpublish_legacy/settings/override/zone.ini.append.php:

[2ZonesLayout1]
AvailableForClasses[]=13479

5. Source: create a new content for the new class, with an 'Item list' block type. Add 'Article 1', 'Article 2' and 'Article 3' to it. Publish;
6. Source: sync;
7. Target: notice order is maintained:

Article 3
Article 2
Article 1

8. Source: edit content, and add 'Article 4', 'Article 5' and 'Article 6' to it;
9. Source: sync;
10. Target: notice order is maintained:

Article 6
Article 5
Article 4
Article 3
Article 2
Article 1

11. Source: edit content, and change article order:

Article 5
Article 2
Article 4
Article 3
Article 6
Article 1

12. Source: sync;
13. Target: notice that the order is not maintained:

Article 5
Article 4
Article 6
Article 2
Article 3
Article 1

Note: this only happens when items are included several times, and then the order is changed. If all items are included only one time, synced, then the order is changed and then synced again, the resulting item order in target is correct.