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The repository settings couldn't be saved.

With Whonix Repository Wizard opening, I choose “No. I will manually update from source code.” option, then click to next, click to finish to close the window. Next time I start it, the setting restored. how do I to do in the command line window and save the settings?

lykedy via Whonix Forum:

With Whonix Repository Wizard opening, I choose “No. I will manually update from source code.” option, then click to next, click to finish to close the window. Next time I start it, the setting restored.

It doesn’t. It’s just a tool. It’s not stateful. Linux generally:
discard what any GUI is telling you and verify the actual configuration
files on the disk.

Verify:

https://www.whonix.org/wiki/Project-APT-Repository#Verify_Whonix_.E2.84.A2_APT_Repository_is_Disabled

how do I to do in the command line window and save the settings?

Yes, Whonix-Check tell me the Whonix stable APT repository is disabled. But sometimes if I get a free time, I want to update Whonix manually, Is the

sudo apt-get update

command recomended?

Insufficient. Instructions for upgrading for users:

When you disable Whonix repository, above instructions would only upgrade Debian packages.

When you disable Whonix repository, you need to manually Whonix packages upgrade from source code.

Whonix Repository Tool does not enable / disable automatic upgrades. Has nothing to do with it. Whonix Repository Tool only enables/disables Whonix repository, i.e. packages sourced from Whonix.