The installer Skyline uses leaves behind the last version it installed, in case you want to revert to that version. If you have both Skyline and Skyline-daily installed that could mean you have 2 stale prior versions of Skyline on your system or 4 total sets of Skyline related executable files.

Probably nothing to worry about, but if for some reason you wanted to achieve a system that looked like you had only ever installed Skyline once and never upgraded, then you would need to go to "Add and remove programs" in your system settings. Uninstall Skyline, where you would be asked if you wanted to revert to the prior version, but completely uninstall. And, then, re-install Skyline.

I think that would give you what you are requesting, but I would suggest rather that you should get used to having an extra version of Skyline around for both Skyline and Skyline-daily, which gives you a little extra insurance, in case you ever do want to rollback, and costs you very little disk space (less than a single high res mass spec file from a modern instrument).

You could also use a different installation strategy:
1. Administrative installer installs into C:\Program Files, but doesn't manage updates.
2. Unplugged installers provide a ZIP file which you can unzip and run Skyline from anywhere you want (ignoring the installation)

Again, I recommend just not worrying about the files you have found. They shouldn't be a problem and are just part of how the auto-upgrading installer works.

--Brendan