I've located the Machinarium,app and I've clicked "Show Package Contents" and I cannot find my saved files. So I went into my Local Host folder and I saw a Machinarium file that I replaced with the one downloaded and now all my progress is lost.
I'm assuming the .sol file you'd downloaded is the one from location #13 (DrainageSewer)? If so, upon starting the game your screen would look like this:

So yes, all of your progress from the .sol file you'd replaced would be lost, but you'll be at the DrainageSewer location where you wanted to be, correct? And hopefully with all three wrenches present (i.e., one on the pipes, one in the book, and one in the drain)?