If I get your query correctly, you have saved some new CMYK files on shared drive and InDesign is only getting old files as option to place on shared drive location ?
If that is correct please check by disconnecting and reconnecting shared drive again .
Not exactly, but if you close the InDesign document (and maybe InDesign too) and then reopen it, wouldn't InDesign need to read/show all mountable files/filenames in any directory you open using the Mount "command"?
If Finder can see all the files why can't InDesign?
Thanks for confirming, this could be due to the permission issues or limited access to adobe applications. Please try to reconnect the shared drive again.
If still does not work please check by moving one or two files to desktop, does that work from desktop?
Also try how it works on root account.
For details click here How to enable the root user on your Mac - Apple Support