Just thought you'd like to know about this little bug.
Sublime Text 2.0.1 build 2217
If I have a file open in another tab, and I alter it in a different editor, then I do a Find & Replace in Files which alters that file, Sublime text uses the in-memory copy of that file and doesn't reload it from disk. If I first focus that tab, then the file properly gets reloaded from disk.
Suggestion: before a find & replace in files, make sure all open tabs are current with any out-of-band changes to their disk copies.