While billing and emailing invoices, there are a few invoices that also need to be mailed because they require additional items (waiver, etc.). Is there a way to tag those clients or projects so that the user gets notified to do this additional step?
There is no notification currently for billing items like this. However, you could create a project or client group for those special cases so that they can easily be isolated and found in the billing process. So you could do a billing cycle for others and then separately for this group.
Another option is using a custom invoice numbering format for such projects. You can add a prefix or suffix to the number such as E (for email) and M (for mail) to indicate that these invoices require additional action. Custom invoice numbering is set at the global level, but can also be done at the project level.