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How about a solution like this:
When you buy augmentations that drops your essence below the next whole number, an entry in the advancement log is added "-1 Magic/Resonance due to essence loss". This entry in the log would be used to adjust the Magic/Resonance.
Much in the same way a log entry is added when you buy gear (focus) and click "Bind".
With a deduction in the advancement log, it should be possible to keep track of the magic score at the time where you wish to buy a new level of magic.
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