I’ve rarely ran into this issue, so, I’ve no details together on how to accurately replicate this and post it as a bug. But, hopefully someone will “if” this is a ST issue and not a flaky plugin that’s in use.
For the ‘refresh folders’ it’s just a command to force ST to reevaluate the projects folder structure, you can execute this command via the Command Palette.
More info about the Command Palette can be found here: docs.sublimetext.info/en/latest/ … lette.html
A list of commands available for Sublime Text 3 (build 3061) can be found here: pastebin.com/mc7aWnsM