The were two accidentally created branches different by case - Int001 and int001 and we couldn't figure out why we don't see each other's changes.

It turns out that it is impossible to make case-sensitive merge on Windows because .\git\refs\heads has only one folder Int001 (or int001, depending what was checked out first) for the branch, and therefore git checkout Int001 or git checkout int001 won't really matter.

The solution for that is

$git checkout int001
$git branch tmp
$git branch -d int001
$git pull 
$git checkout Int001
$git merge tmp
$git branch -d tmp

... and then commit and push