I would now do a Save_As of your Project file.
Shut down the program, and plug the external HDD back in. Open the original Project, and not the Save_As version. Do you get the "Where is file _____.AVI" (or similar) dialog? When you navigate to the external, and to the folder, can you re-link to those files?
I find it a very good workflow to establish a set drive letter for all externals in the OS, so that whenever they are plugged in, one gets the same exact drive letter.
The lesson here is not to disconnect your hard drive while it's being used.
I'd like to re-linking to MTS files with CS6 Premier using MAC Mountain Lion into this thread. This becomes an issue when you are opening a project file sent to you by a collaborator and both of you have the same footage each computer but located on different drives. This requires re-linking the media to match the location on your drive. With the latest update of Mountain Lion, MAC now packages the AVCHD file structure into a single file called AVCHD (with a QuickTime logo). In a standard MAC finder, you can now open this file to reveal all your MTS clips as thumbnails viewable in QuickTime - nice for a quick look at your footage withou having to open it a separate app. You can also right click on the AVCHD file and "Show package contents". This gives you acces to the complete AVCHD file structure down to individual MTS files in the Stream folder.
However, when you are within CS6 Premier and need to re-link a file on the timeline or media browser you are stymied by the AVCHD file. When you try to re-link using the Premier finder window (which looks a lot like a MAC finder window but with extra buttons) you see the AVCHD file. If you try to open it, you get a file type not supported. If you try to open the package (as described above) the only option you get is "Quick Look".
Currently, the only work-around I'm aware of is to rename the AVCHD file in the MAC finder window to anything else. This breaks the connection to QuickTime and allows you access to the full directory structure (you also need to rename the BDMV file to anything else). Now you can re-link files from the Premier timeline since you can drill down to individual MTS files. However, because the AVCHD naming convention starts file names with 00000.MTS for every directory, you need some hint as to WHICH directory the file on the timeline comes from. Also, with this work-around, you have to manually re-link each file. Premier will not pickup other files in the path. I also experimented with renaming the directory back to AVCHD. This does restore the QuickTime icon but not the functionality. Apparently initial renaming breaks a fork that naming it back to AVCHD does not automatically restore. There is probably away to get the fork back, but I haven't found it yet. We updated from Snow Lepeord to latest Mountain Lion as part of our transition from Final Cut Studio 2 and FCP7. We liked the ability to view MTS clips natively in MAC finder. It wasn't until the re-linking requirement that we discovered this flaw.
I've reported this to Adobe support and they have confirmed the problem.They are researching it. In my opinion, the programmers need to add file drill down capability to the Premier link window as the solution. This problem has probably arisen due to Mountain Liion's latest update that packages the AVCHD directory. Premier hasn't caught up to that update.