I'm running ST 3 build 3129 and noticing weird errors in the lists of displayed files and folders in my project. I'm removing a lot of files and folders (as part of splitting one git repo into two parts). As I remove them, ST seems to get confused about what was removed. It will often continue showing a file or folder that I removed, but omit some item (folder or file).
Once it does this, I have not found any way to correct it besides closing the project window and opening a new one. Simply collapsing the project listing and expending it again is no help.
This is on macOS 10.12.4