The Altium file associations are not a problem. I have AD Viewer, CS demo and EAGLE 7.7 Free installed and there are no influences to KiCad with
mod files if you avoid to double click on them.
I think your problem is KiCad installation path. When you just accept every installation steps, you accepted that KiCad will be installed as many other Windows apps in
Program Files [(x86)]. Unfortunately KiCad can't save anything to
Program Files folder and its own library subfolder
...\share\libraries because didn't have higher permissions to do that and pass through the Windows UAC. You didn't get any warning or error on that form Windows. He just do it their own way.
Your modified libraries fortunately has been saved and should be found in Virtual Store which is created for any attempt to save in
Program Files by unknown to UAC application. Enable visibility of hidden files in Explorer and then look at
C:\Users\<your_profile_name>\AppData\Local\VirtualStore\Program Files folder.
To avoid these situation in the future, there are two options:
1. Uninstall KiCad and save your work and KiCad's Virtual Store content. Install KiCad somewhere else than Windows
Program Files and restore your modifications.
2. Keep KiCad where it is and always save your work and libraries outside folders protected by Windows and include these folders in any new project you started. You can create your own portable template using some info in KiCad manual if you choose easy way. Or modify default
.pro file from
\share\templates folder if you choose harder way where UAC will be play first fiddle again.
ps. The Devs should think about add some warning in installer for Windows users. The WinXP era passed away.