manual should be updated: values in XML are pushed to DB.
Any change in the XML file now imply that you should uninstall and reinstall the Theme.
BTW: rather than copying a theme, you should extends it (via Theme Editor)

@LouisGac Good to know, thank you! How can I uninstall and reinstall the theme? I just extended the bootswatch theme and modified the new one!
And yes I extended it from the Theme Editor, I wrote it wrong :)

from the themes list (Theme Box on homepage)

https://manual.limesurvey.org/New_Template_System_in_LS3.x

I just uninstalled and reinstalled the extended theme (extended from Bootswatch), and not only it is still not loading the newly added .css and .js files the config.xml, but it's also not loading the custom.css and custom.js files (which are not empty, as shown in the Theme Editor and confirmed by looking into the server).

I am sure the extended theme is being used and loaded as I tried to put a {{ dump(aSurveyInfo) }} in the layout_global.twig file of the extended theme and when debug is set to 1 it actually prints the result.
But none of the .css and .js files in the config.xml file are not being loaded, they are nowhere in the html file nor they are loaded (checked with Google Chrome -> source)
I tried incrementing the version in version.php, and also setting debug to 1 or 0, deleting the cache and refreshing the page, but none of the .css or .js files in the config.xml file of the extended theme are being loaded.

Is there something I am missing or did wrong?

Nevermind, just uninstalled and reinstalled again, and it worked perfectly... I feel like eventually, this is always the best solution, how could I not think about it in the first place...
I guess something went wrong, I uninstalled the theme and immediately reinstalled it without checking first the survey theme options (i.e setting another theme, and setting back the extended theme once reinstalled)

don't worry: your bug report is greatly appreciated.
the new theme system has a huge level of complexity and abstraction (3 different loops of infinite inheritance), so it could remain some hidden bugs here and there.
so feel free to ask for help to create your theme, to report all the non intuitive stuff, etc

I can see that, I dig deeper into the code, and it's quite complex, but definitely interesting. I switched from 2.7 to 3.0 some days ago, and I must say it was a HUGE improvement, I can modify litereally anything I want. I can get all the information I need regarding the survey, I can now create an index of the survey on the sidebar, customize and use the survey info on the page layout.

I managed to load all the .css and .js files I needed. But It would be nice to add an "update" button to the theme which would be triggered by a version on the config.xml file. Uninstalling and reinstalling the theme to reflect changes on the config.xml file is not intuitive!

If I may add, the .css and the .js file which I added in the config.xml file do not appear under the file list of the theme editor page!

yep an update button is a good idea.
can you create a feature request?

Version 3.3.0 released

The problem still exists local. It seems only to work on production.
If I try to develop themes locally to push them on production, I use $php -S localhost:8000.
But the custom.css file is still missing. I do the same as discribed above. With debug mode on, the same problem.
In head it has the custom.css from vanilla and not my own from upload/themes/...
This is only a problem with custom.css. Theme.css does work.

Big_Lemon:

if you're using the Theme Editor, the save button now regenerate the assets:
https://github.com/LimeSurvey/LimeSurvey/commit/bcda36f1170d6ffeae88003a34eb0b4b48f99c3b#commitcomment-27500363

If you're not, you will now find a button to regenerate the assets in global settings:
https://github.com/LimeSurvey/LimeSurvey/commit/b6df690ecac2a456443fed60c5c191b0cef827d0