This isn't fixing itself - these pages are getting entries for both namespace=0 title='MOS:whatever' and namespace=126 title='whatever', rather than the latter replacing the former. For an example page I happened upon today, and tried unsuccessfully to fix by briefly removing the MOS: link entirely:

MariaDB [enwiki_p]> SELECT pagelinks.*, linktarget.* FROM pagelinks JOIN linktarget ON lt_id = pl_target_id JOIN page ON page_id = pl_from WHERE page_namespace = 10 AND page_title = 'R_from_short_cut' AND lt_title LIKE '%NOPIPE';
+----------+-------------------+--------------+-----------+--------------+------------+
| pl_from  | pl_from_namespace | pl_target_id | lt_id     | lt_namespace | lt_title   |
+----------+-------------------+--------------+-----------+--------------+------------+
| 39507473 |                10 |      5543400 |   5543400 |            0 | MOS:NOPIPE |
| 39507473 |                10 |    101191794 | 101191794 |          126 | NOPIPE     |
+----------+-------------------+--------------+-----------+--------------+------------+

@Anomie gives a query against the real tables in T71222#742492, though that's now very out of date (actor table, at minimum).

Only about 43 per day - we're losing the pages that would have been created by ips, but registered non-autoconfirmed users were still creating drafts on 11/5 after the temp-account rollout.

The more immediate problem than the repetition - as reported in both current duplicates - is that if you add a title and then either blank it or replace it with whitespace, it doesn't go back to "Click to add title..." on the query's page (example) and "Untitled query #54382" at /query/runs/all and the user's list of queries, it's blank on all three, and it's unclickable on the latter two.

Since you've already solved \^ and [^charclass], and lucene doesn't support backreferences anyway, rewriting ^ to "[" + START_ANCHOR_MARKER + "\n\r\v\f]" at query time (and similarly for $) should be equivalent, right?