If a client already has a mandate setup in GoCardless, there is currently no way to link that to the client record in Kashflow, so taking payments needs to be done outside of raising the invoice in Kashflow.
Speaking with support, there are only two ways round this.
1. Create a new mandate.
2. Create a new mandate, but tell the client to ignore the email and contact support to then make the link.
At best, these options are unnecessary and would cause confusion for clients. At worst it damages trust - Trying to set something up on their bank account that already exists with call telling them to ignore the email about it is likely to raise suspicion.
There should be the facility to link clients to existing mandates in GoCardless. Either through a manual drop-down list, or perhaps an automatic match of the Kashflow client code and a GoCardless custom meta field.