I've been searching around about this for a while, but I haven't come across much. I don't believe I'm the only one having encountered this problem. For example, see this post, which describes the exact same issue in detail, but which has not gotten any response: https://forum.sublimetext.com/t/folder-case-sensitivity-confusion/6717/1
Since that time, the issue has persisted into Sublime Text 3 beta (not using dev builds). My particular problem happens using SSHFS, but I have ruled out any issue with either my local machine, the SSHFS driver, or the remote filesystem by using Terminal and Finder commands outside of ST3, which is able to see the files in question.
Specifically, I have a code tree containing a directory which then contains two subdirectories, 'Test' and 'TEST'. ST3 seems to believe that files which actually exist in the latter of those directories are actually in the former, then attempting to open them (or search), and failing to do so.
This is a pretty pernicious bug which effectively prevents me from accessing an entire subdirectory of this particular directory structure. Has anyone else encountered this issue or had any way to work around it? Thanks in advance.