>I just found out that the package has taken all VFP deleted records on the process. How can I make sure that the deleted records are not imported into SQL Server? Or, should I have pack all my tables before doing the import?

Use a linked server based on ADO. Then all is easier using OpenQuery (and it automatically drops deleted ones - in fact with this approach you have problems if you also want the deleted records).

EXEC sp_addlinkedserver 
    @server = N'VFP_SERVER',  -- Your linked server name here 
    @srvproduct=N'Visual FoxPro 9',  -- can be anything 
    @provider=N'VFPOLEDB', 
    @datasrc=N'"C:\PROGRAM FILES\MICROSOFT VISUAL FOXPRO 9\Samples\data\testdata.dbc"'


insert mySQLTable (orderId, orderDate,shippedTo)
Select * From openquery(VFP_SERVER,
'Select
  order_ID,
  Cast(Evl(order_date,Null) As DateTime) As order_Date,
  TRIM(to_Name)
  from customer')

Linked server has 2 primary advantages in your case:
1) It automatically drops deleted
2) OpenQuery allows you execute VFP syntax for VFP and SQL syntax for SQL side.
Cetin