I would think it is illegal. If your name is on the paperwork you are the "pilot in command" of the aircraft. If another pilot actually flies the trip and the paperwork is not changed then i guess technically there is not a legal flight plan on file. i would even go furthur to say your company would open themselves up to the almighty "command and control" bag of worms....................................
The flight plan is not "the paperwork." In fact, when ATC sees that flight plan, they don't have a clue abou the PIC, alternates, anything else. Of course, you're talking about a situation in which the FAA takes a closer look...in which case it still comes back to who the certificate holder has designated as the PIC.
What exactly is the almighty command and control bag of worms?
So far as a legal flight plan on file; the company may use any means designated and approved by their POI for flight tracking...which isn't necessarily an FAA flight plan.
Certainly in considering a case in which the PIC of a given fligh isn't clear, the FAA will look at the flight plan to help clarify who was acting as PIC. However, in the case of a flight plan in which the company changed PIC's and the listed person isn't even aboard the airplane...clearly that person isn't the PIC, and it's a non-issue.
The pilot designated for the flight should file his own flight plan or ammend the existing one, but this isn't a show-stopper, nor a crucial issue.
"The paperwork" will be any company generated paperwork regarding the flight, and may include manifests, aircraft logs, dispatch sheets, and other records as appropriate to that operator.
I had a boss that would file flight plans under different names. His idea was that it would allow him to go over his flight time if he needed to.
That is an intentional act and fraudulent misrepresentation. It also is a stupid act, and doesn't save the offending boss, because the flight plan isn't evidence that he did or didn't make the flight. It is evidence, however, when combined with other evidence that he's committing fraud and falsification. The FAA takes a very dim view of that.
Because of this I seriously think that the FAA would take it pretty serious if they found out that people were taking flights with inaccurate flight plans.
Non-sequitor.