Can one have two pedidos de permanência on two basis

Yes, you can start a new Pedido de Permanência Definitiva com base em cônjuge brasileiro(a). What you need to do is to advise the Federal Police when you apply that you wish to cancel the other one based on stable union. (Arquivamento de Pedido de Permanência com base em união estável).

Actually it is much to your advantage to do so, since the stable union application DOES NOT automatically carry with it the right to obtain a work permit (Carteira de Trabalho e Previdência Social - CTPS) and to work during the process as applications based upon marriage or having a Brazilian child do.

The other great advantage of the application based on marriage is that for Constitutional reasons it really can't be denied. In theory they could deny a VIPER based on stable union, as long as the marriage is legal and there is neither a de facto or judicial separation, you would never be denied the VIPER on any grounds.