If you open Windows explorer and navigate to where your company files are (usually under Documents\QuickBooksCompanyFiles) and you double-click on the file that has your company file's name and extension ".qbw", is your computer launching QuickBooks 2020 and opening that company file? Or do you get the same error message as you saw in ProSeries?
Your first step would have been to set up the "link" to your company file. When you did menu Tools->QuickBooks Billing/Customer Update->Set Preferences and clicked the "Browse" button and chose your company file, did you, at that time, not received the message that it couldn't find the correct version of QuickBooks?
Since then, did you re-install QuickBooks?
Is the menu Tools->QuickBooks Billing/Customer Update->Set Preferences still showing the right file and in the right location on your hard drive?
I'd say to change this setup to link to some other QuickBooks company file (make one up with fake data just for this experiment) and see if you can push your invoice data to that company file.
Then close/reopen ProSeries and change the setup back to your company file and try to push invoices again.
"Should I try and move my Quickbooks file to another directory."
No; it's not just that one file that is used. QB has a relational database, so it is the .qbw + linked utility files.
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