You had an old master, with your testCols commit on top. Then you merged upstream master into it. Then you pushed that merge commit to upstream, accidentally.
When you 'fixed' it, you made the testCols commit the new master. This discarded all the changes from the upstream master. (from the last day or so)
Luckily this doesn't seem to happen very often. To make this less likely, I recommend you do not pull from upstream master manually, and you instead have a sh/batch file that runs: `git pull upstream master --ff-only` which will fail loudly if you have made changed in your master branch (rather than silently creating a merge commit).
As for CRLFs, I recommend turning git's autocrlf off, so git no longer messes with your line endings.