When making progress with endurance sports you will have periods of ups and downs (but hopefully on average if you have been training properly mainly ups). A part of these down are periods of illness, so what is the best way to return to training and begin making progress again?
Avoid high intensity training when returning for 2-3 days.
First workouts back should be short and low intensity.
Allow the body to mostly recovery before training.
Take training day-by-day till you feel recovered.
Physical active in general will improve your immune system, however, there is a small window of immune suppression after training (particularly after high intensity workouts). Often these are the causes of illness resulting in athletes temporally pausing their training.
But what about getting back to training. Well the thing you should know is you are unlikely to lose all your fitness. The body is able to store your condition, so the fitter you are the quicker you can get back, meaning you will not need to start from scratch. Of course, it depends on the severity of the illness, but in general you should restart training from the previous couple weeks, and make sure your first couple workouts are short and low intensity.
For example if I am on week 5 of a ten week program I and I got ill, I would start again on week 4 or 3 depending on how I was feeling. I would then avoid intervals for the first 2-3 days. However, what if you are mostly recovered but still have some symptoms of illness? This is something that must be judged on a case by case basis, but the best practice is taking your training day by day. For example with BCA athletes, if they were ill by feel mostly recovered we will take the training day by day till they (and myself) feel comfortable we can resume as normal.
The biggest mistake you can make however, is restring to early with training that is to hard. Although it may be frustrating, making this mistake can lead you long term health issues. So be patient and remember as frustrating as it is, getting ill is an inevitable part of the process.