From my limited understand of encryption in Duplicacy, the master password simply decrypts the config file on the storage, and can certainly be changed.
The hash/chunk encryption keys (there’s four of them) stored within that config file can’t be changed and there isn’t a CLI option to re-encrypt. Those keys are pretty strong though, and randomly generated.
I can see why someone might need to re-encrypt the whole shebang - say if the initial master password was weak - someone with an old copy of the config file might be able to brute force the config and then unlock the data. But if they’ve got your weakly-encrypted config file, they’ll also potentially have copies of the chunks and can crack them at leisure, regardless of if or when you re-upload.
Just choose a good master password; long, completely random with symbols and store it in a password manager. If the previous password was weak and your storage resides in a cloud drive, purge old versions of the ‘config’ file after changing the password.