I am still encountering the same issues.  I have found that if I save the file as a new file name, it will keep the changes.  However, any additional changes after the filename change require the file to be saved again as a different name until complete.  Ultimately once all changes are complete, I rename the last file back to the original file name before submitting electronically to the IRS/States.

I have contacted support and they are indicating no one else has reported this issue.  I recommend reporting it to support so they do not consider it an isolated incident.