To calculate earned revenue, I pull the invoice information out using report writer, use excel to separate the date out formulaically and spread the revenue over the service period. Unfortunately this causes some difficulty with merged invoices.
This will combine all the individual invoice line items into a single invoice deleting all but one of the merged invoices. Unfortunately if the invoices that are being combined are from a previous period I will again have the invoices in the system twice, once from the prior period and once for the merged invoice. Changing the status of existing records is not a good internal control.
I would suggest merging invoices should be an option assigned to the customer account, not something to be applied by customer service. If the account has the merge invoice feature turned on a master invoice would be created with sub invoices as part of that invoice. This allows the customer the functionality they desire of seeing and paying one invoice, but with the detail of multiple invoices