Quickbooks Online to Desktop Export - Missing Data

The export to desktop has known problems, known for over a decade now, many things do not export or export incorrectly.  There is really nothing much you can do about it.

I would start a new company file in desktop for this year, use the balance sheet from QBO to get your starting balances and move forward.  Use the QBO reports to fill in the block on the tax form you file for 2019

The only real option to get all your data for archiving, or to use in a desktop import program like transaction pro,   is to have an accountant log in and print or export to excel the general journal. (Or invite yourself as the accountant, create the log in, and log in as the accountant so you can use the accountant tools.) Due to QBO's limited data handling capability that will probably have to be done in date segments. Of course that may not help in the event of an IRS audit since they have stated that the actual software data file is what they want, and an excel spreadsheet is not satisfactory.
(Note: simple start does not have a true general journal report at all.)

QBO data handling capability for reporting is not adequate, if there is more than 5K records it times out and reports that you have too much data. You will have to do a journal report in date range segments, like Jan-Feb, Mar-Apr, etc etc.
How many months you can span per report is a guessing game since the report can not deal with more than 5K transactions.

We had a few clients similar to your case. We had them purchasing a 3rd party conversion service. Should you interest to explore it, send us your email address in private message. We will foward it and you will make a deal directly to them.

If you are running QBD in multi-user mode, consider deploying a private cloud solution. Mix your LAN users and mobile users to work on the same file at the same time.

https://partners.myquickcloud.com/?pc=fiatlux

Thanks for the advice Rustler!

I was leaning in that direction but wanted to take one last swing at it.  As of right now my plan is (for anyone who may be interested):

Step 1: My move was only 5 months ago so I am using a product called SAASant which can transfer all my data to spreadsheet form.  I have the import into desktop software as well, but have to many errors to clean up when I go this route. So Step 1 is to get my data our of Quickbooks online all the way back to the beginning and from when I made the switch (9/1/19)

Step 2: Use SAASant to import the changes to my lists into the original quickbooks desktop I still have from the move.  I recommend keeping a backup of that file just in case you need to start over.  So far the importing of the lists went off without errors in a few minutes.  Transactions seem to be different issue.

Step 3: If you don't have a lot of data or maybe it is better categorized than mine you may be able to import all your transactions without a problem.  I don't seem to be so lucky.  So I'm taking those spreadsheets and doing manual entry where I have to and then using information I can download (credit Card expenses, bank account info, etc) to just re-input the data.  

So far that is the plan for the next week.  I figure I can work out of that file since I'm doing manual entry of all the other data and can control everything.  Maybe even take some time to clean up things after 10 years of just inputting data instead of really planning how the books will help my company run.  

I will post an update when it is all said and done!