dholloway,
I think you will find that you will be apply your ticket to a higher fare ticket.
Regarding receiving miles on the US BA Exec Club, there are actually some fares that do NOT receive any miles.
No, I am pretty sure that they will NOT allow you to get miles for flights that are not flown. Call them and ask.
In addition, the more you pay does not necessary mean the more tier points you receive. You only receive more tier points for traveling Club, First or Concorde.
For bonus miles, it is blue=1, silver=1.25, gold =2.
Hope this helps!