I found a workaround to this.  If you don't use a standard QBO format, it seems to work for some reason.  Meaning you can import missing transactions without it turning off automation.  

It will take you to a mapping screen.  You'll want to say "First row is header" and make sure that the right columns match description, date, and amount.  If it's a format that QBO recognizes even if its CSV, it seems to want to turn automation off for that bank account.  

• Create a CSV (See attached) with Date, Amount, and Description. 
  
  

• Note the positive and negative and that it's in one column
• Click on "Link Account" and then click on "Upload from file" on Banking Screen". Click Next.
• Select appropriate bank account account.  Click Next
• Select your CSV and then click next. For mapping do the below:

• You should be gravy now!  Accept your transactions and it should still work in an automated fashion!