Hi @asmeedhungana,
We can use a factory to deploy upgradeable contracts. We can also make the factory upgradeable, though upgrading the factory only changes the factory and not any of the already created contracts by the factory.
To upgrade contracts deployed by the factory, the admin of each contract would need to upgrade the contract, we could do this programmatically. As the contracts weren’t deployed using the CLI we wouldn’t be able to use the CLI for this. I wouldn’t recommend trying to manually modify the CLI config to be able to upgrade using the CLI.
I suggest not using App.sol: When should I use App.sol in my project?