When SCons linting fails, the linter gives bad advice about how to fix the issue; it says: 

To fix formatting errors, run pylinters.py fix <path to file>

But this won't work, as I learned through trial-and-error. In fact, you need to run 

pylinters.py fix-scons <optional path to file>

to fix the issue (similarly, you need to do lint-scons rather than just lint to see lint failures for SConscripts).