One important thing to realise is that Merge Replication (MR) requires that both the publisher and subscriber databases are in sync. This is achieved through the application of a snap-shot file or through 'forced-replication' (search this site to found out more) if the databases contain different datasets initially.

If synchronisation starts and the two databases are different, then MR will perform a delete in the subscribing database, as in your case, to make the subscriber to be in-sync with the publisher. Once both databases are in-sync (both tables are clean), then adding records in either the subscriber or publisher will be propagated to the other. This is the two-way nature of MR.