Cannot apply retainer on all invoices

User is able to apply retainer against one billing record in Create Batch Invoice screen, but not to other billing records.

This is because the retainer is for a specific project (project retainer), not for all projects of a client (client retainer). To resolve this, you must delete the retainer payment and receive it against the client instead. In some cases, you might have received the retainer payment against a phase. In that case, your issue can also be resolved by accepting it as the parent project retainer instead. 

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