1)
SQLYog works with more then 2 databases?
answer is NO! But you may 'aggregate' several sync jobs to a batch file. Refer: http://webyog.com/fa…-same-time.html
2)
SQLYog tells me the it will overwrite primary keys in case of conflicts, is there a well known workaround for that?
answer is that you will have to define the Primary Key in such a way that the same PK-value is not created on different hosts at the same time. A simple solution to that is to add to the PK of every table a column that is constant on same server but different between different servers. SQLyog is not a magician and it cannot read users' mind. The meaning of the PK in relational databases is that it uniquely identifies rows/records/tupples of a table.