Rather than toy with SetWarnings or confirmation options, the best solution
is to use a Delete query followed by an Append query instead of a Make Table
query.

By designing the table ahead of time (rather than using a Make Table query),
you can define the data types you want: which fields are integers, longs,
double, which are text, which are date, and so on. You can also set the
properties (e.g. set Allow Zero Length to No, which is set inconsistently
(depending on your version) by a Make Table query.)

The code to populate the table then looks like this:
   Dim db As DAO.Database
   Dim strSql AS String
   strSql = "DELETE FROM Table1;"
   db.Execute strSql, dbFailOnError
   strSql = "INSERT INTO Table1 ( ...
   db.Execute strSql, dbFailOnError
   Set db = Nothing

For further info about the code, see:
   Action queries: suppressing dialogs, while knowing results
at:
   http://allenbrowne.com/ser-60.html