I'm having the same problem with BofA Corp and Employee accounts not downloading all transactions in QBO.  The one card uploads all transactions, but he employee card only uploads the payments received and finance charges.  No purchase transactions posted.  It appears as though this problem is not fixed. 

Unfortunately for me, I did not discover this issue until just now and apparently all of 2019's transactions for the one employee card were not uploaded so none of those expenses were filed with 2019 taxes.  Now, with the Oct. 15 tax filing deadline 10 days away I have all of 2020 transactions from the one card to figure out how to download so I can deduct expenses.

Pending a fix of this issue, I've discovered it's a nightmare to convert from Excel to CSV format so the uploading file process will work as promised by QBO.  Converting to CSV does not delete photos or other unnecessary data from the Excel file, so I'm having to manually delete all that data.  Also, the columns are jumbled in the CSV converted documents so when mapping the data from my document to QBO's upload specifications, there is nothing to match to it, so I cannot make this happen.

I cannot believe this continues to be a problem for QBO customers... for two years!!  I will now be late with filing my taxes.  Yes, I was down to the deadline anyway due to issues... but now I'm really screwed.

I'm looking for other bookkeeping software.

Thanks for nothing.