Yeah, if you have access to that folder, you can just copy wherever. The characters they're linked to won't always be so obvious, though. Nonetheless, the file might be something like as2384 or jd9221. Moving them all technically wouldn't hurt anything, but with some changes that have come to the macro system and such since you've likely been gone, some settings may be outright reset, anyway.
Yes, it is a little annoying trying to figure out which is which. Two things I did notice though: first, characters on which you have done more and/or have more macros on will have larger files. It is pretty easy to differentiate my main character from my town-dwelling mules. Second, they are named in the order that the characters were created. I assume SE assigns a unique identifier for each character when the files are created, so if you made the characters at different times, and remember the order you made them, this might also help to figure out which is which.
Or just dump the files in your target folder and see what happens.
"We are Dragoons, and to make short work of foppish cavalry is our bread and butter."
-Bob Shaftoe, The System of the World