The situation may have been caused by the IDE that you are working with. The possible scenario, AFAIK may have been this :
1- You have deleted the four files ( dashicons.eot, .svg, .... ), from your IDE, which probably has a git plugin to track the changed files.
2- After some time, you changed those file and added them again, but either the IDE git plugin hasn't synced yet or you have restored them from outside of the IDE.
To see what a final valid result for git tracking in these files would be, I recommend :
git reset <file-name>
to unstage changes to be committed for <file-name>
or just simply
git reset
which will unstage all file that were staged with git add
, either in the terminal or by the IDE plugin.
Then,
git status
I assume you should now see that your files (dashicons) are modified, not deleted
Now you can add them again and commit your modifications and no deletion will be applied to your repository, both local and remote.