I totally agree with you.  Other accountants I spoke with said the same - mainly if the bank account changes which seems to happen a little more often due to clients' accounts getting hacked.  I called ProSeries to see if I was doing something wrong.  She remoted in, and saw my issue.  She said that she felt I did have to go into the return to update it, and then efile the next estimate when it appears in pending view.  She mentioned I could request this enhancement to the program, but I'm not sure where I go to give them requests for program improvements.  In the meantime, my process is this:

1. I efile the return, and the 1st estimate

2. After return and 1st estimate is accepted, I have to open the client's file, click on the state tab to go into the NYS return to allow it to update

3.  I can either efile from this view or close it and go into efile view to efile the 2nd estimate.

4.  Once second estimate has been approved, I have to go into the file, go into the State return to allow the update to process

5. I can now efile the 3rd estimate

You can see how this can become a long process.  Keep in mind, we now have to remember which clients had estimates set up for them.

I will suggest to my boss that we do not do estimates this year unless we keep a list to know which clients to go back in to.