Try to make a "filter compare" beetwen your Architect and Publisher export. Problably is that.
I've noticed that sometimes objects or lines don't appear properly in publisher and I am not sure why.
The following snippet of code shows you how you can update the published database.
var oBusinessPublisher=Context.getComponent("BusinessPublisher"); oBusinessPublisher.updateExport(ArisData.getActiveDatabase(), bpServer, NAMEOFTHEPUBLISHEDDB);
Have you tried publishing with the Entire Method?
I published with this method ...
Here is what has worked for me in the past. it is cumbersome but it worked.
Step 1. Go to the process models in Business Designer and delete the links which are currently not displayed in Publisher.
Recreate those links and save the process model and log-out
Step2. login into the Business Architect. Use Administration Module; go to Your Database Server>>Publish>>Publisher Server>>Server
Then select the Relevant Export from the list in Exports Tab displayed on right.
Once you select the particular export the "Update" button will get enabled; use it to update the export.
Step3. Relog-in into the publisher and you should be able to see the links now.