I found the solution.
It turns out the projects included in the board consist of all the projects the filter searches over, and not just the projects that actually appear in the result.
My full board query was `project = my_proj AND (statusCategory != Done OR updatedDate > -2d AND status = done) ORDER BY Rank ASC`
This meant the filter going over all the projects...
I modified the board filter to `project = my_pro ORDER BY Rank ASC` and moved the other conditions to the sub filter in the board settings
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