If both the vin and engine number were changed, then it should be obvious that they did it. Not sure about other states, but CA puts both numbers on the title. If you do an engine swap, you have to get it inspected by CHP and get a new title. Same with a frame swap, but one of them has to match the old title.
If both were changed, you’d need some sort of proof that you own it. Something like aftermarket parts you’ve replaced. Try getting serial numbers from the manufacturer for those parts, something to prove it is yours.
94mm bbk, +4 stroker, Hot Cams, Vertex piston, FMF Power Bomb header and Power Core can, KW black diamond valves/dual springs, FCR39, K&N, Elka long-travel LT fronts and rear, Houser +3, +3/4 LT A-arms, American Star pro xs chromoly tie rods, Dyna non-programable, Tusk +3 axle.