@Vinny *******
, you need to understand that there is a HUGE difference between a real VISA and an extension of stay.
A year-long, multi-entry Non-B visa (that you get ONLY from a thai consulate OUTSIDE the country) requires that the holder exit/re-enter the country every 90 days for the validity of the visa.
A year-long extension of stay (that you get ONLY from the thai immigration office INSIDE the country) requires that you do 90 day reporting
You don't need to do anything if she is canceling the VISA, just cancel the work permit, exit the country, get a new visa from a thai consulate.
However IF she is on a yearly extension, you need to cancel the work permit, take that receipt and paperwork from her company to the immigration office and CANCEL the extension of stay she's on. You don't need to wait until the last day you can go weeks early. They will cancel the current extension and stamp her in until the termination date on the paperwork. Then you can leave the country and go get another visa.