Gmail doesn't have the Send and Delete or Send and Archive button when you reply from a non-Inbox folder. It is a known-oddity that many people complain about. However, you can achieve almost the same thing easily.
After replying, you can archive from a folder by clicking the Remove label button (or if you use Gmail keyboard shortcuts click y). Archive in Gmail simply means having all labels removed except for All Mail. So when you are in your Inbox, archiving means removing the Inbox label.
If using Gmail not in your browser (i.e., your phone, Outlook, etc.), after replying, you can simply drag and drop an email to your All Mail folder to archive.
Or if you'd rather, you have two other options:
1. Drag and drop that particular email into your Inbox if the email is one you are likely to respond to. This will train SaneBox to deliver future emails from this sender there in the future, and you will also then have access to the Send and Delete and Send and Archive buttons.
2. Click the Once button in your digest or star the email which will cause us to put the email you want to respond to into your Inbox, and you will have all your favorite buttons available to you.