I'm not sure what you are asking. MC does not move or copy media files. When you import music files, they stay where they were; MC just knows about them after import.
Audio analysis just reads the files to determine volume levels, etc. MC then writes the volume level information into it's internal database. Fields like [Volume Level (R128)]. If the file being analyzed supports it, Media Center will write those tags back into the metadata of the file. FLACs support a lot of metadata and will normally get these tags written into them.
You can look at the tags on a file, including the volume level info, by opening the Tagging Window. Edit > Tag
I hope that helps.
Brian.