Leaving him to cry when he is ill and suffering from separation anxiety is (in my opinion!!!) only going to make bedtime more stressful amd upsetting for him.
The quicker he realises you come when he cries and won't just leave him upset and scared, the quicker he will learn that there is nothing to be scared of.
Leaving a baby to cry when all they want is the reassurance you are there, will only make them realise that you aren't there and it will take him much much longer to get over the anxiety.
I know it's easier said than done. I've often been so exhausted and frustrated that I wanted to just leave ds to scream at bedtime but in the long run, I know it wouldn't have done any good.
I stayed at the side of the cot, with m hand on him for a while til he was calm and dozing off. Now he's 11 months and I just have to pop him in his cot and stand in the door so he can see me. It takes less time, no crying, happier ds and happier mummy!
For what it's worth, if he sleept well in his cot before the separation anxiety then he should return to sleeping well once he feels secure again.
It is hard though but it does pass and all he wants is to have you close. I couldn't leave my ds to cry knowing that all I have to do is cuddle him or let him see me and he would be ok.
Especially while he's ill. When my ds had a cold, he was scared as he couldn't breathe well through his nose and laying down made it worse. I propped his cot up at the top end on a few books and cuddled him til he got over it.
A cold can make us feel very poorly so for a baby that doesn't understand it's just a cold and it will pass, it must be scary!