Currently, MapInfo Pro only supports deleting one open Geopackage table at a time from the same GeoPackage (GPKG) file.
To delete multiple tables from a single GPKG file, open and delete each table in turn. If you delete multiple open tables, then each of the tables is unavailable for use by MapInfo Pro, but the table data remains in the GPKG file.
You can delete an open GeoPackage table by using the Delete Table command on the TABLE tab in MapInfo Pro. Deleting a GeoPackage table deletes the TAB file and all associated component files. If a GeoPackage has only one table, using this command will delete only the table and associate files, not the GeoPackage file.
For more information, see Deleting a Table.