The augmentation dot consolidation is incorrectly changing the vertical placement of the dots.
Is there any way to move augmentation dots vertically?
Unfortunately not at the moment.
Here a workaround to have the dots where you probably would like, in this situation:
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Hide one of the dots (you can choose to hide the dot from the bottom E if you prefer):
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In a separate voice (Up-stem voice 2 in my example), insert a note with suppressed playback and hidden notehead and stem (the dot remains visible).
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Set the Voice column index of the various voices to obtain the desired result:
Dorico file example:
fake rythm dot positioning.dorico (1.3 MB)
That’s smart!