A newly-created indexed file containing zero records (or an indexed file from which all previously-existing records have been deleted), will have size zero in the data portion but will occupy at least 3K in the .idx portion.   Why is that?

The 3K or more of data held in the .idx portion of an empty indexed file is header information necessary to define the file.  The header information includes the primary key position and its length (or the position and length of each of its pieces if it is a split key) and its data type (numeric or character).   It also includes the position, length and type of each of the alternate keys, as well as other defining information about the file.

For indexed files of type MF"8" a.k.a  IDXFORMAT"8", the data portion and index portion are held in one disk file.  This one file will show at least 3k even when the file contains zero data records; this 3k is the header information.