I use ST2 2109 (OS X) and I think that ST overwrote one of my project files with another, which is pretty annoying because I had all my file/folder exclusion pattern set and I lost them (well, I can get it back from time machine I guess). I can’t really say how it happened because I don’t know when it happened exactly.

I have multiple projects all in the same folder “~/src” and I often switch between them using Ctrl+Cmd+P. I don’t think it’s my fault (like, for example, using “Save Project as…” and overwrite) because I never use “Save Project as…”, I edit project files “by hand”.