User.sys is loaded from the HOME by an “automatic loading of modules” entry that is created automatically and is visible in sys params, base.sys is loaded in the same way but the entry is not visible or editable.
Base.sys is loaded from the release directory into all tasks, so the correct way to load it would be to save the changes to the file on the disk and then P-Start the controller, that should ensure that the correct version is loaded into each task.
In general, I think that the intention is that you should avoid modifying base.sys, especially on your PC, because you may inadvertently download a change that does not apply to all robots.
The preferred approach would be to have your own system module/routines, encrypted if necessary, that would execute your code from a shelf routine rather than modifying base.sys.