Sorry you suffered this issues. I can see a few hundred Wikibase\UpsertSqlIdGenerator::upsertId errors at that time.

In particular to:

INSERT INTO `wb_id_counters` (id_type,id_value) VALUES ('wikibase-item','1') ON DUPLICATE KEY UPDATE id_value = LAST_INSERT_ID(id_value + 1)

I will send this information to wikidata team and CC @Ladsgroup , as that count could be a contention point. However the error didn't repeat itself in the next 17 hours, and corrected itself after a few minutes, so maybe it was just the typical bot going out of hand creating new items and not leaving anyones else resources to do the same (something that it is common on Wikidata). It could also be related to a temporary issue with the new version deployment: https://wikitech.wikimedia.org/w/index.php?title=Deployments&oldid=1814619#deploycal-item-20190124T2000

I can see an increase activity on enwiki, and notification messages. I can also see that the automatic overload checkers kicked in and solved the issue automatically in a few minutes, so, - in a way - something was already done to "fix" it (the query killer takes care of bad database states).