Check the script, see what it's doing. If there are fewer rows after than before, then something in the script you are running is deleting data. Probably your merge script has a section which deletes old rows.
SQL will not automatically remove data from a table.
Gail Shaw
Microsoft Certified Master: SQL Server, MVP, M.Sc (Comp Sci)
SQL In The Wild: Discussions on DB performance with occasional diversions into recoverability