New Post: Problems with model after upgrade to 6.1

I have a large model using code first with migrations

When i create a new migration i creates all the indexes again, and canot apply them because they already exist.

public partial class VerUpdate : DbMigration

{
    public override void Up()
    {
        CreateIndex("dbo.AcumuladosArtigos", "ArtigoID");
        CreateIndex("dbo.AcumuladosArtigos", "ArmazemID");
        CreateIndex("dbo.Armazens", "EmpresaID");
        CreateIndex("dbo.Empresas", "CodigoPostalID");
        CreateIndex("dbo.Empresas", "PaisID");
        CreateIndex("dbo.CodigosPostal", "LocalidadeID");
        CreateIndex("dbo.Localidades", "ConcelhoID");
        CreateIndex("dbo.Concelhos", "DistritoID");
        CreateIndex("dbo.Ruas", "CodigoPostalID");
        CreateIndex("dbo.Configuracoes", "EmpresaID");
        CreateIndex("dbo.Configuracoes", "CentroCustoPredefinidoID");
        CreateIndex("dbo.Configuracoes", "ContaBancariaID");
        CreateIndex("dbo.CentrosCusto", "EmpresaID");
        CreateIndex("dbo.CentrosCusto", "Armazem_ID");
        CreateIndex("dbo.ContasBancarias", "EmpresaID");
        CreateIndex("dbo.ContasBancarias", "ContaSNCID");
        CreateIndex("dbo.ContasBancarias", "BancoID");
        CreateIndex("dbo.ContasSNC", "EmpresaID");
        CreateIndex("dbo.ContasSNC", "ContaSNCID");
        CreateIndex("dbo.AcumuladosContas", "ContaSNCID");
        CreateIndex("dbo.AcumuladosContas", "CentroCustoID");
        CreateIndex("dbo.LancamentosSNC", "EmpresaID");
        CreateIndex("dbo.LancamentosSNC", "CentroCustoID");
        CreateIndex("dbo.LancamentosSNC", "DiarioID");
        CreateIndex("dbo.LancamentosSNC", "DocumentoID");
        CreateIndex("dbo.LancamentosSNC", "DocRelacionadoID");
        CreateIndex("dbo.LancamentosSNC", "ReciboID");
        CreateIndex("dbo.LancamentosSNC", "PagamentoID");
        CreateIndex("dbo.LancamentosSNC", "PagamentoDespesaID");
        CreateIndex("dbo.LancamentosSNC", "CaixaID");
        CreateIndex("dbo.LancamentosSNC", "DocDespesaID");
        CreateIndex("dbo.LancamentosSNC", "ContaSNCID");
        CreateIndex("dbo.LancamentosSNC", "DesignacaoContabilisticaID");
        CreateIndex("dbo.LancamentosSNC", "MovimentoCaixaID");
        CreateIndex("dbo.Caixas", "EmpresaID");
        CreateIndex("dbo.Caixas", "UserID");
        CreateIndex("dbo.MovimentosCaixa", "EmpresaID");
        CreateIndex("dbo.MovimentosCaixa", "CaixaID");
        CreateIndex("dbo.MovimentosCaixa", "CriadoPorID");
        CreateIndex("dbo.MovimentosCaixa", "EntidadeID");
        CreateIndex("dbo.UserDepartamentos", "UserID");
        CreateIndex("dbo.UserDepartamentos", "DepartamentoID");
        CreateIndex("dbo.Entidades", "EmpresaID");
        CreateIndex("dbo.Entidades", "ContaClienteID");
        CreateIndex("dbo.Entidades", "ContaFornecedorID");
        CreateIndex("dbo.Entidades", "ContaUtilidadesID");
        CreateIndex("dbo.Entidades", "PaisID");
        CreateIndex("dbo.Entidades", "SituacaoID");
        CreateIndex("dbo.Entidades", "MeioPagamentoID");
        CreateIndex("dbo.Entidades", "CondicaoPagamentoID");
        CreateIndex("dbo.Entidades", "ExpedicaoID");
        CreateIndex("dbo.Entidades", "ZonaID");
        CreateIndex("dbo.Entidades", "IsencaoID");
        CreateIndex("dbo.Entidades", "VendedorID");
        CreateIndex("dbo.Entidades", "TipoQuotaID");
        CreateIndex("dbo.Entidades", "UserID");
        CreateIndex("dbo.Entidades", "AlteradoPorID");
        CreateIndex("dbo.Cartoes", "EmpresaID");
        CreateIndex("dbo.Cartoes", "EntidadeID");
        CreateIndex("dbo.Cartoes", "CriadoPorID");
        CreateIndex("dbo.DescontosCartao", "EmpresaID");
        CreateIndex("dbo.DescontosCartao", "CriadoPorID");
        CreateIndex("dbo.DescontosCartao", "CartaoID");
        CreateIndex("dbo.DescontosCartao", "DocumentoID");
        CreateIndex("dbo.Documentos", "EmpresaID");
        CreateIndex("dbo.Documentos", "TipoDocumentoID");
        CreateIndex("dbo.Documentos", "ArmazemID");
        CreateIndex("dbo.Documentos", "ArmazemDestinoID");
        CreateIndex("dbo.Documentos", "CentroCustoID");
        CreateIndex("dbo.Documentos", "CartaoID");
        CreateIndex("dbo.Documentos", "IsencaoID");
        CreateIndex("dbo.Documentos", "ProcessoID");
        CreateIndex("dbo.Documentos", "CriadoPorID");
        CreateIndex("dbo.Documentos", "EntidadeID");
        CreateIndex("dbo.Documentos", "MoradaFacturacaoID");
        CreateIndex("dbo.Documentos", "MoradaCargaID");
        CreateIndex("dbo.Documentos", "MoradaDescargaID");
        CreateIndex("dbo.Documentos", "DocPaiID");
        CreateIndex("dbo.Documentos", "DocFilhoID");
        CreateIndex("dbo.Documentos", "ViaturaID");
        CreateIndex("dbo.Documentos", "VendedorID");
        CreateIndex("dbo.Documentos", "ExpedicaoID");
        CreateIndex("dbo.Documentos", "CondicaoPagamentoID");
        CreateIndex("dbo.Documentos", "FormaPagamentoID");
        CreateIndex("dbo.Documentos", "AssinadoPorID");
        CreateIndex("dbo.Documentos", "UserId");
        CreateIndex("dbo.Documentos", "ImpressoPorID");
        CreateIndex("dbo.Documentos", "ReImpressoPorID");
        CreateIndex("dbo.Documentos", "ExportadoPDFPorID");
        CreateIndex("dbo.Documentos", "EnviadoPorEmailPorID");
        CreateIndex("dbo.Documentos", "MotivoAnulacaoID");
        CreateIndex("dbo.Documentos", "AnuladoPorID");
        CreateIndex("dbo.Documentos", "DocDespesasTransporteID");
        CreateIndex("dbo.ComentariosDoc", "EmpresaID");
        CreateIndex("dbo.ComentariosDoc", "DocumentoID");
        CreateIndex("dbo.ComentariosDoc", "UserID");
        CreateIndex("dbo.CondicoesPagamento", "EmpresaID");
        CreateIndex("dbo.Ficheiros", "ProcessoID");
        CreateIndex("dbo.Ficheiros", "DocumentoID");
        CreateIndex("dbo.Ficheiros", "EncomendaID");
        CreateIndex("dbo.Encomendas", "EmpresaID");
        CreateIndex("dbo.Encomendas", "EntidadeID");
        CreateIndex("dbo.Encomendas", "ProcessoID");
        CreateIndex("dbo.LinhasEncomenda", "ArtigoID");
        CreateIndex("dbo.LinhasEncomenda", "EncomendaID");
        CreateIndex("dbo.Artigos", "EmpresaID");
        CreateIndex("dbo.Artigos", "FamiliaID");
        CreateIndex("dbo.Artigos", "IvaID");
        CreateIndex("dbo.Artigos", "IsencaoID");
        CreateIndex("dbo.Artigos", "UnidadeID");
        CreateIndex("dbo.Artigos", "TipoImpostoID");
        CreateIndex("dbo.Artigos", "FornecedorID");
        CreateIndex("dbo.Artigos", "UserID");
        CreateIndex("dbo.Artigos", "AlteradoPorID");
        CreateIndex("dbo.Artigos", "ClassificacaoSNCID");
        CreateIndex("dbo.Caracteristicas", "EmpresaID");
        CreateIndex("dbo.Caracteristicas", "ArtigoID");
        CreateIndex("dbo.Caracteristicas", "TipoCaracteristicaID");
        CreateIndex("dbo.TiposCaracteristica", "EmpresaID");
        CreateIndex("dbo.ClassificacoesSNC", "EmpresaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaSNCID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaIsentaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaDevolucaoIsentaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaIvaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaIvaDevolucaoIvaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaDevolucaoID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaDescontoID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaSegundaMaoID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaEspecialID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCustoID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCompraID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCompraIsentaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCompraIvaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCompraDevolucaoID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCompraDevolucaoIvaID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaDevolucaoDescontoID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCompraDescontoID");
        CreateIndex("dbo.ClassificacoesSNC", "ContaCompraDevolucaoIsentaID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaSNCID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaIsentaID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaIvaID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaIvaDevolucaoIvaID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaDescontoID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaSegundaMaoID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaEspecialID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaCustoID");
        CreateIndex("dbo.ClassificacoesSNC", "IntraContaCompraID");
    etc.......

How can o resolve this?