Well, no, they didnt. But apparently upgrading to powershell 4.0 does nuke all of the user modules, which sucks.
So. Step 1. Re-Install amazon modules (I just installed everything)
Open new Powershell window and run:
Get-Module -ListAvailableStep 3.
Step 4. - Setup your private keys again. Oddly enough that part actually still works. So, hitting the ec2 commands works right after reinstalling cmdlets.
Step 5. If your creds were not carried over, or you never configured them, take a look at my earlier post