I have distributed an app on a lot of ipad in my company. I did this with developer profiles on the ipads. Now I have re-distributed the app with iOS Developer Enterprise Distribution. For this I used a new apple developer account, certificate, app id etc.. Now I see that the newer version of the app does not overwrite the older version but installes it besides the older version.
How does the ipad decide if an app needs to be overwritten by a new one? Is this the app id? If so, can I use the same app id with different apple developer accounts?
As far as I can understand your problem.
Your first distribution was with an iOS Developer Program and a Development Provisioning Profile with name com.mycompany.myapp
Your second distribution is with an iOS Developer Enterprise Program and a Distribution Provisioning Profile with the same name com.mycompany.myapp
You are expecting that, because they have the same name they are the same, however they don't have the same name.
Every Provisioning Profile have a 10 alphanumerical Unique Identifier for every Developer Program.
Then your first Provisioning Profile could be something like*: VGHU6789JHY.com.mycompany.myapp* and the second 879JHYUJ8H.com.mycompany.myapp. You can check that in Xcode / Organizer / Devices / Provisioning Profiles.
You can ask Apple to migrate one Provisioning Profile from one account to another. Takes time, but it is possible.