FileMerge is way over my head... help!

I'm NOT a developer.
I downloaded XCode to get FileMerge after it was strongly suggested to me to sort out the mess that happened after a corrupted disk wouldn't go back to it's original state... In other words, I had made a clone of that disk prior to said corruption, and when I tried to clone the cloned image (or is there another way to copy it back to the first disk?), I noticed a huge gap in data size... and very quickly I could notice that not all files were transfered.

Now, I know not all files are cloned when you clone a disk. But interestingly, what happened wasn't that weird files I don't understand didn't transfer... it was the CONTENT of folders that were missing. The folder would be there and at first I'd think it got cloned back fine... but it would say 0kb. And if I tried to open it... there was indeed nothing there.

Since we're talking about my iTunes library and about 500Gb of data, I didn't feel like checking every entry manually... and that's where FileMerge comes in.

First I loaded both drives for the comparison. It took about 24 HOURS to complete the initializing process. I wish I had known it would take that long, otherwise I might have just done it manually after all!

Then, I realized I had the option to check what was different and correct it manually... or use the MERGE option.

So I chose MERGE.

In my weird logic, it meant that all that was different on one drive would be changed on the other... and since there had been no modifications, I figured it would simply mean all the files that didn't originally clone back, would finally be transferred, and I could FINALLY, after about a week of fiddling around, get my drive back... and be able to start over the work I had lost when the drive corrupted (the small part that had not been backed up-cloned).

But it's been almost 48 hours now that FileMerge has been running to MERGE... still processing.
I have no idea in what order it's working, doesn't seem to follow a logic I can see, so I have no way of knowing if it's close to finishing or not. My cursor is the spinning beach ball when I put it over the program, but the Status is changing in the status bar (the file being processed is updated), altough very, very slowly.

I wouldn't dare quit FileMerge while it's working on the drives, as if something were to happen, I would lose all I have left!

And to make everything really, really bad, I just opened the original drive (the one I'm trying to get in good shape, the one I was trying to clone back to and merging was to get the missing files to that drive...), in Finder... and it says 0 files. There is nothing there according to Finder.
But it does say about 500Gb are used. They just don't show.

So... did that merging stuff just ERASE that drive instead of actually putting everything that was missing ON IT???

I know, I know, it's all my fault... I shouldn't have tried to use a program that I didn't fully understand, and messing with files is touchy.
But that program had been so strongly suggested, nowhere had I read a "be careful" and even though I'm not a developer, I'm not a noob about computers either... (if I had been, I would've just lost all my data a week ago when my drive got corrupted, wouldn't have had a backup, wouldn't have spent so many hours trying to get back those files in so many ways... wouldn't have known where to look for FileMerge).
But I'm thinking I played with a program that's way over my head and now I'm worried.

So basically what I'm asking is should I quit FileMerge? Is it normal to take so long merging the files? Because it's not built for that?
If I quit while it's doing it, will it just stop, or might it corrupt data?

And please explain how come merging simply removed everything... (but where the heck is everything, by the way? still on the drive but hidden from the Finder?!)

Thanks a ton!