
Something about her is attracting the male, so on that basis alone, I think I'd have the vet take a look, just in case there is infection going on. And if she's having a phantom, I'd seriously consider getting her spayed. If it's happened once, it may well keep happening, pulling her down. Somehow lactation with a false pregnancy seems to go on and on - far longer than if there were puppies!
Yes, by all means keep them apart - she doesn't need to be bothered by him when she'll not be feeling that great in any case. But do get this checked by your vet just in case (thinking Pyometra, maybe?)