I'm no expert but just wanted to say I know how you feel. When I'm out for more than 3 days unless planned I start to feel like I've lost control of my whole life. Luckily, that hasn't happened for about a year now (unplanned rest that is !).
Possibly, your immune system was working extra hard during your illness which may account for loss of muscle.
Best you can do is look forward to getting to where your were and then going beyond that. Sometimes these unplanned breaks can up your motivation even more than before.