At the moment I’m rather ill and my body is in pain, but I don’t want to loose muscle and flexibility by not doing my daily workout. Any advice to keep going without hurting my body too much?

I Would Recommend performing seated exercises or stretches that don’t involve applying intense pressure on the body. You Could start small seated exercises and if you can you could try performing low-intensity standing movements that lightly stretch and lengthens your body. This is not proven or expert advice, but you can try this recommendation for yourself and listen to how your body feels and responds to very light movements. I Hope you get well and just try and see how it feels. 😇

Gentle and mild stretches/workouts are a better idea. If you are up to weight lifting, go for a much lighter weight than usual. Yoga can also work as both a workout and stretching (so it counts as exercise). Make sure to modify EVERYTHING and EVERY SINGLE EXERCISE you do.

Just a little bit of active stretching, or yoga, helps a lot, especially with your flexibility.
Focus on your breath, while doing so, and it's going to work as some kind of meditation.
About the muscles, don't worry; periods of time where you don't train as much, or where you completely stop, are actually going to benefit you during your fitness journey.