Editing a file outside atom instance causes issues when reopening

Steps to reproduce:
1) open atom with `atom .`
2) open styles.less
3) quit atom
4) move directory
5) open atom with `atom .`
6) delete parts of styles.less
7) quit atom again
8) return to the first directory
9) reopen atom with `atom .`, causing styles.less to be opened automatically
10) Colours are highlighted in the wrong places.