It seems that there are many outdated source folders in the C:\Program Files\WindowsApps directory.

[DuckDuckStudio]

There are multiple Microsoft.Winget.Source folders under C:\Program Files\WindowsApps. They appear to be outdated sources.

Can I delete them? Will they be regenerated later via winget source update?

[JohnMcPMS]

You should not delete them yourself as they are under the control of Windows packaging. They should be cleaned up naturally, but obviously there is some issue with that happening on your system.

Do they contain files, or are they just empty folders?

[DuckDuckStudio]

I randomly checked several directories, and it seems that they only contain Public\index.db.

Edit: There are also some empty folders.