I will want to synchronize 2 databases in one but the synchronization operation deletes the records from the destination database which are not in the starting database how to eliminate this problem
Hello joel ferdy thank you for choosing ApexSQL,
This is a very uncommon scenario for ApexSQL tool's usage, the tool was designed on a 1 to 1 model, however this process could be achieved but with some extra manual steps.
Here's what I suggest (Also, I'd recommend doing a test run before performing this task):
Option 2: Use T-Rep to SQL Server Many-to-One replication
This process is better explained in this article that uses SQL Server to perform the many-to-one replication you're looking
Hopefully this information will help you achieve your tasks.
Have a nice day!