Not sure if this CAN be handled, but essence is increased when you remove cyberware. character can never regain essence due to bioware/cyberware (escept for some fairl rare and radical procedures in Runners Companion? So when yu add or update your 'ware there is an essence "hole" that can be filed with additional 'ware with no essence penalty.
Also AFAIK by RAW you are also supposed to track essence lose from bioware and cyberware separately. Never had a game come up where a char had both though so it might be a corner case.
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