Suffice it to say that amended routes can occur for just about any reason, flow restrictions, weather, local traffic (within one facility's airspace), preferred routings...anything.
For example...take any original filed route....let's say KDFW GARL6 TXK MEM J42 ORW.ORW7 KBOS. For some reason the plane gets vectored after leaving the northeast gate so that he is now off the departure due to flow restriction 800 miles away. Then a flight progress strip prints out on the aircraft with a TMU reroute that says...
+CRAMM BNA+, if it is a preferred routing (pre-programmed into the system and widely used) or simply...
CRAMM BNA J42 ORW.ORW7 KBOS. In either case the "J42 ORW.ORW7 KBOS" part is common to both routes so the amended clearance would read...
"Kingair 34C, cleared to Boston Logan Airport direct CRAMM Nashville then as filed" or
"Kingair 34C, cleared to Boston Logan Airport direct CRAMM Nashville, rest of route unchanged" or, more likely
"Kingair 34C, Proceed direct CRAMM Nashville, as filed", sort of short cut phraseology.
The point being that the "then as filed" or "rest of route unchanged" would begin at the point where the amended route picks back up at a common point with the original filed route (if it does, otherwise it would essentially be a completely new route). A computer generated reroute will join the two parts, but if the controller takes you off a routing for some reason on his own then it will be up to him to eventually give you a clearance that will result in you joining up with the filed route somewhere ahead.
If the SID connects to the filed route then the clearance from Ground will read...
"Kingair 34C, cleared to Boston Logan Airport Garland 6 departure Texarkana, as filed" and sometimes though not entirely correct...
"Kingair 34C, cleared to Boston Garland 6 Texarkana as filed".
If the flight strip has "FRC" printed on the bottom then the controller must read the entire clearance as it is printed as a full route clearance.
Of course, generally the airlines will get their clearances via ACARS with their pre-departure clearance. But this is how it works with clearance that are read manually.
tex