I'm sorry that you're having difficulty. As Jim mentioned, MC does not, under ANY circumstances, move files without explicit user interaction. It is possible that you moved them without understanding what you were doing, I suppose, though you would have likely had to work at it quite a bit.
If you'd like assistance, we'll need more information on what happened, where the paths were, if the files are actually on disk, and generally a bunch more details.
The Conversion Cache feature does not move files, it creates copies. The idea is that when you sync to a handheld, and MC needs to convert the files in order for the handheld to support them (or just to save space, etc), it can cache these converted files "off to the side" so that next time you sync the same files over, it doesn't have to do the conversion again. This, obviously, greatly speeds up future syncs if the vast majority of the files have already been converted and just need to be copied over to the device again. This convenience comes at the expense of disk space, of course, because it makes copies.
When MC makes a converted copy that it stores in the cache, it generally imports the converted file and "stacks" it with the original source file. More info:
http://wiki.jriver.com/index.php/StacksMC will
never automatically move files into the Conversion Cache (or anywhere). And it will never delete the source files when you do a handheld conversion. It is possible that you found the duplicates and were confused and deleted the sources. It is also possible that you have the Stacks expanded (which makes each copy show up separately) and you just happen to be looking at the duplicates in the Conversion Cache directory, rather than the sources.
Essentially, the only ways to make MC move files are:
1. To use
Library Tools > Rename, Move, and Copy Files.
2. To manually move the folders or files yourself in Drives & Devices under the
Tree.
3. To manually change the [Filename] field in MC's database for a file or set of files.
All of which require you to do something explicitly to move them.