AutoFilter is limited to showing the first 1,000 unique entries in its
drop-down list. To de-dupe another way, use another column for a
COUNTIF function. In it put

=IF(COUNTIF($A$1:A1,A1)1,"X","")

and drag down to copy to the end of your list (assuming your list is in
column A).

Now autofilter on that column for X to get duplicates and delete them,
or Autofilter on blanks to get the uniques and copy them elsewhere.

HTH

DOR