I have the same exact problem.  Duplicate transaction appear, just moments after they were already reconciled.  And I also bank with chase.

Was your issue resolved?  

Recently Chase rolled out a new connection platform for online banking.  I received an email requiring me to adopt this new system interface, which forced me to start using the Advanced Bank Feeds option, verses the Classic Mode I used prior.  Never had this issue before I updated to their new platform.

This problem adds a LOT of wasted time to reconciling my accounts, as it takes twice as long to go through each transaction to weed out the duplicates.  Need a solution.

QB desktop 2020