But this still doesn't take away the need to create a backup. If I run 1099s through QuickBooks Desktop I have to create a backup, correct? 

If I create a backup, I can no longer send those changes to my 30+ clients who send us an Accountant's Copy, correct?

This means, if you are an accountant, that you cannot run 1099s in QB unless you want to re-do the work every year, correct? 

I just want to make sure I am not missing something - I know you stated to answer Yes, but I am still answering Yes in the backup file, not the accountant's copy, so any changes made in the backup will not go to my client. 

Very frustrating - I cannot believe this is the process and I know other accountants will be frustrated with this as well.