Well, this MAY not be your experience, but what I did was to search for files that I KNEW weren't connected to my PC - they reside on an external Firewire drive and I had NOT connected that drive - yet. And, yes they appeared with a red line through them. That is what should happen.
So I then connected the drive and they still remained "Offline". OK, I'd expect that. I then used the Media Manager Options - this is located within the Drop Down menu on the MAIN MM Search Results Toolbar. In this Drop Down I clicked on the "
Media Library" tab and
without checking the "
Ignore files dates . . " I hit the UPDATE button. Be warned this takes time!! Mine took a good 10 minutes - first time around, but then it was quicker.
After it had finished all the previously red line files were "seen" as being online.
Now, I ain't suggesting that this IS your experience, however, if you think about it, Media Manager will NOT know you have changed the files you are NOW using within a project. Yes, change the file names. Yes, substitute these files with those that you had previously used. But how would MM know you had used these files, with new file names, instead? All I'm suggesting is that an update may just do that for you? Yeah?
As I said, with my experiment, I
FORCED an update after I reconnected my drive. Maybe this experiment was unnecessary as,
IF, I had had the External Drive connected in the FIRST place I would have had success anyway??!?

But having done the Update process it DID resurrect the files when I did a search.
Now, there IS a Default setting that you might wish to check. I bet it IS checked, as you haven't said files and usage AREN'T being updated - see? Anyways have you this engaged or not:
GO >> Options > Preferences > General > "
Save media-usage relationships in active media library"
I need to experiment MORE with MM - I really should - it is a VERY powerful and for me a truly valuable asset in this suite of software.
Grazie