I'm also having a similar issue, but I'm either doing something wrong or my situation is a bit different.
I've got a shiny Rayquaza that keeps getting the "Invalid: Encounter Type PID mismatch" error. If I change it to a PID from RNG Reporter it will then spit an additional error on top of the previous on which is "Invalid: PID should be equal to EC".
I tried the reverse method for putting in the PID in PKSM, but it's the same result as above.
The PID it has is FF80D403. I don't know if that's the original PID as I'm not to one who altered this Pokemon. All IVs are 31 which I'm not sure if I can just adjust those to whatever they originally were and boost them legitimately at a later time.
PKSM has an auto legality function, but I really do not want to utilize it as it wipes a lot identifying data like origin game, ribbons, etc while making it appear to be from Ultra Space. Normally I wouldn't care, but as dumb as it sounds this specific Pokemon has a lot of sentimental value to me, so I'd much prefer to avoid that.
Edit: It still let me transfer it through Bank into modern hardware. I don't use online functions, so non-issue.
