I have Table A with the following values:
+------+------+
| ID1 | ID2 |
+------+------+
| 1689 | 1709 |
| 1709 | 1689 |
| 1782 | 1709 |
| 1911 | 1247 |
| 1247 | 1468 |
| 1641 | 1468 |
| 1316 | 1304 |
| 1501 | 1934 |
| 1934 | 1501 |
| 1025 | 1101 |
+------+------+
+------+------+
| ID1 | ID2 |
+------+------+
| 1641 | 1468 |
| 1911 | 1247 |
+------+------+
How about: (not too sure whether this works in SQLite)
DELETE FROM TableA
WHERE EXISTS (SELECT *
FROM TableB
WHERE TableB.ID1 = TableA.ID1
AND TableB.ID2 = TableA.ID2)