I agree. My strategy would be to treat it as if you have a legit bike with no paperwork, and some separate papers which have just become irrelevant. As others say, the knack is in finding a real human at DVLA to chat to. Can they confirm that your (real) frame no and engine no are NOT stolen or scrapped? If so, should not be a bother getting age-related plate (not transferrable, but not Q). Think a dating letter from Honda is about £50. I assume/hope that at one point, SOMEONE had at least 2 VT500s and bikes and papers got mixed.
If ithelps, I once bought TWO RD250DXs (yeah, I know). I got papers for a THIRD one, one of the ones I had but with a different engine no, NOTHING with the sellers name and address on it, and papers to prove the sale of one bike to someone else!! Phew! Both bikes off road for five years plus. After a WHILE, I got thru to a lovely anorak who just went thru what I a tually had, and we straightened everything out. At no cost, I got all the papers for two bikes I owned (I guess nothing was nicked).
I wont tell you the story about the TWO T140s in Scotland with the same frame no......
Good luck. Be honest and inmocent (and lucky) and I hope you will find the right person to talk to. TELL them how much time and effort you put in. And tell us when it works out.