As someone living with MECFS, thank you for asking this question.
In short, I'd say work on the basis that your job share partner won't be able to step back into the role as before. Depending on severity, many people with MECFS cannot work at all, as just surviving the day takes all their available energy.
As PPs have so eloquently described, MECFS is a devastating condition, and very poorly understood especially as people don't look ill. There are levels of severity, but even 'Mild' MECFS is defined at losing 50% capacity. While people who are 'Mild' can sometimes do some work, it often leads to long term deterioration in their health.
While recovery from Post Viral Fatigue is possible, once you have been ill for a year, it's likely you are in MECFS territory, where full recovery is unlikely. Some people do improve but it is often slow and unpredictable and most people actually just plateau, functioning at a much lower level than before.
If I were in your shoes, I'd be thinking about how to ensure you are protected as it's unlikely your job share partner will return at full strength, if at all.
I appreciate that makes it harder to emphasise with what she is going through but it's great you are trying. MECFS is a truly awful condition, made even worse by being disbelieved and dismissied by others.
I have found it shocking that I have become disabled, there is no health care at all, no treatment and yet people think I can will myself better, as if MECFS is some sort of character flaw. It's not, it's a biological disease, with a proven genetic component, often triggered by a viral infection, and research has shown it has a greater disease burden than (for example) MS.
I think because it doesn't (in the main) kill people, it isn't seen as that bad. But it has taken away my ability to live my life, work, move around, maintain a normal social life, think straight, so many things. Chopping that carrot sums it up. It sounds bizarre and ridiculous, but that's what MECFS can do to you.
💐 💐 💐 to my fellow sufferers and those with loved ones blighted by this cruel condition.