AMA linking to the files doesn’t actually do anything to the files. The original files should be the same as they were before you linked to them.
The qt’s you created out of avid are probably in a codec that FCP can’t recognize…perhaps an avid dnx codec?
If you are pointing FCP to the original files, on the external drive, and they are coming up green, there is a chance FCP can’t work with that codec either. You haven’t said what your original files are.
I would suggest going back to Avid. If you no longer have your AMA links, redo those and transcode the media, and continue on in Avid. If you still have working AMA links, start transcoding.
If you need to output for FCP, you will have to try a couple of different codecs untill you find one that works for you. In the end it will probably be quicker to transcode and stay in Avid. Outputting a whole bunch of of self contained quicktimes for use in FCP isn’t going to be a fast process.
You could also try running your footage through Resolve and create proRes files, but again, it could take awhile, depending on your amount of footage.
Glenn