When a user is deleted, reputation of users voted by the deleted user will change.
From https://askubuntu.com/help/user-was-removed I see
This removal occurs whenever a user is deleted, unless that user had a very high reputation score.
That's a bit vague, is there a limit or does someone decide from case to case what exactly a “very high reputation score” is?
Update: The help text got revised. Its last paragraph now correctly states:
We have a system in place that examines the impact of removing a user's votes. If the user has cast a large number of votes, deletion will be held up so staff may consider preserving the votes prior to the deletion. The decision is at the staff's discretion and cannot be reversed after the deletion has taken place. If you are seeing a "User was removed" event in your reputation history, it implies that the user either hadn't cast enough votes to be reviewed, or staff made the explicit decision not to preserve the votes.
Original answer: The latest "official" post about this which I could find was this Meta SE answer by Shog9 from 2015. I would personally summarize it as:
The system checks the impact of removing a to-be-deleted user's votes, examining both the total number of votes cast as well as the votes cast against individual users.
If either exceeds a potentially site-specific, non-disclosed threshold (all he said there is that it's "pretty low"), the deletion will be put on hold and requires a manual moderator review. During that, it will be ensured for example that the user was not involved in voting fraud. If that is not the case, votes will be preserved.
This post doesn't say anything about a threshold regarding the to-be-deleted user's own reputation. My guess is that this was the old filter (before 2015) which turned out to be not that effective.
The FAQ post about this was also very recently (couple hours ago) edited to mention the number of cast votes as criteria for whether votes will be preserved or not, instead of the reputation count. So probably all the help pages are wrong for a couple years now and nobody noticed yet until today :)
Actually earlier today Stack Exchange employee animuson clarified (quoted, emphasis is mine):
"High reputation" is a generic way to explain what happens that isn't super confusing. A help center article isn't meant to go into all the explicit details, but rather just highlight the generic functionalities. Users get held up based on their number of votes and/or the number of people they've voted for. Reputation is not actually considered at all in the check.
