"Open with" configuration gets screwed up unpredictably on El Capitan
I would suggest you rebuild the LaunchServices database, the mechanism which matches files to the apps which open them.

There are several sites which explain the process, here and here, for example.

In essence, you need to copy and paste the following command in Terminal after making a full backup with Time Machine:

/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain u -domain s -domain l -v



If you are leery of using Terminal, you can use the free app Onyx to rebuild the index. Onyx has many other abilities in addition to rebuilding the LaunchServices database.

Disclaimer: I have no financial or other stake in Titanium Sofware, the developer of Onyx.