Each file that gets “fast imported” into Media 100 gets an ID written into its QuickTime header. This is how Media 100 can decide which of 2 clips with identical names is the right one to use.
There is no “easy” or official way to link to new files. But (in case you are somewhat adventurous), I did something for a project lately where I was facing similar issues.
What I did was to export an XML from the timeline I wanted to relink, and then manually (or with a find/replace command for groups of clips) I did replace the media file filepath in the XML file via a Texteditor. Then I used the “update Media from XML” command to link to the new files while keeping the edits and effects intact.
Make sure to make a copy of your timeline before doing the “Update Media from XML”, because it will replace the clips on your current timeline; it does not create a copy or something.
If you have questions, juts post them here.