In an unfortunately frustrating loop here. This issue started occurring in Xcode 5 about a month ago and I have just been dealing with it hoping that it would go away with Xcode 6 but I'm still seeing it happen in the current App store release of Xcode 6.
When visiting the "Accounts" tab in Xcode, then tapping on an account and clicking the "refresh" button to download the provisioning profiles for that user, instead they all get invalidated. Then I have to go into the developer portal and manually regenerate each one. The only way to get the valid profiles is to download each one manually from the developer portal onto each of our machines which is not ideal. Is there a reason this is happening that I'm missing? I've never had this issue before. If it matters, these are not the default team profiles, we made and manage our own.