Do you mean changing a statement from one property to another across a whole wikibase?

So more steps to reproduce:

Say if I merge Q2 into Q1 and I query all records containing statements with Q1 should items that refer to Q2 show up. It appears that https://www.wikidata.org/wiki/User:KrBot does the maintenance here. But no code is shared.

@Addshore does this help?

I think this issue should get more priority so I'll try to be extra clear :)

You have a Wikibase full of entities (e.g. Persons)
You have an item about a person 'Alice' (Q789)
Alice has a statement Father P90 'Bob' with item Q456
Q456 appears to be a duplicate of Q123
Q456 is merged into Q123

If I now query 'give me all persons where Bob is the father':
SELECT ?person WHERE {
?person wdt:90 wd:Q123 . #Q123 being the new Q-number for Bob
}
I do not get Alice. I only get Alice if I query
SELECT ?person WHERE {
?person wdt:90 wd:Q456 .
}

This can lead to dangerous false negatives. Less dangerous in the humanities but maybe in wikibases that related to gene research.