(Mac keyboard shortcuts, ST 2.0.2)
cmd-shift-f (in menu, Find > Find in Files) brings up the 'Find / Where / Replace' tool as pictured, which applies to all open files
cmd-alt-f (in menu, Find > Replace...) brings up a more traditional 'Find / Replace' that only targets the currently focussed file
So, use cmd-alt-f (Replace...) instead of cmd-shift-f (Find in Files) to avoid this problem.
Customer support service by UserEcho
(Mac keyboard shortcuts, ST 2.0.2)
cmd-shift-f (in menu, Find > Find in Files) brings up the 'Find / Where / Replace' tool as pictured, which applies to all open files
cmd-alt-f (in menu, Find > Replace...) brings up a more traditional 'Find / Replace' that only targets the currently focussed file
So, use cmd-alt-f (Replace...) instead of cmd-shift-f (Find in Files) to avoid this problem.