Hey there,
it's not really possible to tell what's happening based on your post alone

Looks to me like a bunch of different issues that snowballed from a single problem initially, but can't really say what that might have been. I suspect that there was an error during package install, which should have been in the logs right after installing it - if you restarted the editor since then, it's probably gone now.
What might help figure out what's happening is if you upload your
PackageConfig.xml as well as
ApplyUpdate.xml (if existing) and take a screenshot of your
Source/Packages folder contents. No guarantees, but it's worth a try.
If you're using source control (if not, that
should be a ToDo!) go back until the error disappears, otherwise you should be able to recover the previous state of your game using the Backup folder that Duality maintains. A fresh re-install (Delete
Source/Packages entirely, then start the editor) could also help, but only if
PackageConfig.xml isn't broken.
When you install the package again after recovering the previous working state, copy
logfile_editor.txt and
logfile_editor_prev.txt to somewhere safe, immediately after Duality auto-restarted to apply the update. If there's something broken again, these are the two files we need to figure out what went wrong.