You can design your package in a way to figure this out.

Use a sql task to query and stuff the resultset into a variable

IF EXISTS (SELECT * FROM NewDatabase..Table)

SELECT MAX(IDentityColValue) AS MaxVal FROM NewDatabase..Table

ELSE

SELECT 0 AS MaxVal

Set a variable in the package for the MaxVal.

Then in your data flow.

Source Query will be

SELECT <ColumnList> FROM OldDatabase..Table WHERE IdentityColValue > ?

And set the Parameter to feed in the MaxVal Variable.