MobiLink: How to add a new table to synchronisation using Sybase Central and mlagent
This seems¹ to work: 


Create a new Remote Schema Name (e.g. v2.0)
Do changes on your consolidated database (e.g. CREATE TABLE-statement)
Update schema inside your synchronisation profile and maybe increase version string (on my current test it appears to doesn't matter)
Do a deployment of your update synchronisation profile. You will need update ml_columns and ml_tables as well as ml_table_scripts etc on your consolidated database fitting your update synchronisation profile. So apply the changes to it. Also you will need the SQL of remote database
Create an upgrade remote task including the remote SQL created with step 4 (EXECUTE SQL). This task should also change Remote Schema Name
Maybe iterate your sync- task and deploy both -- upgrade task and sync task
Should be done


The biggest issue is, that the script in default is droping the tables on remote side so a huge amount of data might be transferred after update. 

¹ I was able to get this running on a local test scenario with minimum database.