Grain of salt here: I don't use EF, and usually recommend people avoid EF.
Anyway, the error seems pretty self explanatory. If EF does not support the "Server" keyword in the connection string, then don't use "Server". Since this is a database upgrade, presumably you are using Code First EF, and so the first connection string you used when the database was first created did not use the "Server" keyword. If that assumption is correct and EF were self-consistent from creation to upgrade, then someone must have introduced that "Server" keyword later. Ask whoever added/modified to connection string to deal with the upgrade problem. (Granted, one of the reasons why I don't use EF is because I kept on hitting bugs in EF, as well as there were places where it was not self consistent.)