Say hello to an un-documented side-effect of "rep recalc":
We (as user) shouldn't know anything about this internal stuff, but it appears a reputation recalc cannot take into account votes from questions since then deleted...
And a large "rep recalc" seems to be underway following some mishaps with a "bonus" to be set when associating accounts...
As mentioned in my question, we do not care about all that: we just want the rep back.