If you update qty values via GeekSeller interface or via a file upload, and after 1-2 hours those numbers change automatically, it means you have turned on quantity synchronization for nodes which you are updating.
You can visit GeekSeller dashboard > Extension > Amazon to check which of your nodes are linked to your FBM or/and FBA, and if you have qty synchronization option turned on.
In order to keep this synchronization on, but still be able to provide your own qty information about inventory levels you have in your warehouse but are not listed on Amazon, you can add additional node in your partner.jet.com panel. This additional node will be used for your manual updates of qty, while the other nodes are linked to your Amazon.
After you add a new node to JET Portal, to see in it GeekSeller you need to go to GeekSeller > Settings and Refresh Nodes.