Hi Cameron,
You say 'forever altered' as if it's a tragedy but with some cigars it's a blessing :).
Yes, the flavors change but it also depends on how long it's been out. If you like those changes, smoke it else pitch it. If you can, tamp and remove as much ash before putting the pipe down because the ash, pipe tobacco or cigars, retains ammonia.
Once out (cold) you have to remove all ash from a cigar and as much ash as possible from the pipe (hard to get it all). Before lighting, blow firmly through the cigar and gently through the pipe to disperse the ammonia.