I also support a triple-check for uploading the config itself. The issue sme experienced is, I think, in no way his/her fault - the rest of Sublime Text's configuration system works by using the config files as a layer over safe defaults, and that was a perfectly understandable mistake to make. Anyway, wbond: would it be possible for each sftp-config.json to check whether or not it has a copy of itself on the server, perhaps during the routine check against the server that individual files do when opened? It's very likely that it would be mirrored to the same remote directory, so could probably safely just check one folder. Even just once every day or something would be a great safety net.
Anyway, fantastic work with the plugin! I use it countless times a day for work and it always functions beautifully.