[kevin rhoades]"Is this going to haunt me later?
No. The ".new' suffix is to help you tell the original clip from the transcoded copy. Avid does not link by file name...you are free to change it. If you make the Source File column visible in your bin, you will see that Avid keeps track of the original source file name you transcoded the new clip from. There are a few people out there spreading nonsense about the ".new" clips..but they are wrong. This is how its supposed to work. If you know how to use the Relink dialog, everything should link up later to the original file.
There is one big limitation. When you transcoded, did you change the frame rate? If you did, you will get a warning that you will not be able to reconnect. Heed this warning.