OK if a song is listed in 'All tracks' and no where else then it's considered unattached?

I think you mean "if a song is listed in all tracks but not in a playlist". See, if it's in All Tracks, and you've got your tags filled out, then it probably also appears in Years, Artists, Albums, and Generes. Those are the "soup" views, automatically built from the song's tags, and they are not related to the REFS count.

If that's what you meant, then yes. When the song is listed in one of the "soup" views but not in a playlist, that's when it's considered unattached and its REFS count should be zero.

So I copied the 'unattached' song into the playlist it should've been in and all is well right? No problems doing that right?

Right. You've now given a homeless song a home.

I know the best way would be to re-upload the file but I can't the original is gone.

No, the best way would NOT have been to re-upload. If you had done that, then you would have had two different copies of the song on the player's hard disk. You did the correct thing.