It just means your old Melmetal was probably always illegal to begin with, it's just PKHeX wasn't updated to deal with it.
So you can use an old PKHeX, but just know your Melmetal would still be illegal, even if it appears legal on an older version.
New PKHeX added various ball (LGPE vs GO->HOME) and date legality for GO mons.
So that probably is the issue you're facing. Wanna make a Melmetal, then make sure all conditions are satisfied.
The GP1->LGPE->SWSH is probably your best bet, since the date of capture is correct. You just need to ensure the other details, such as ball legality, matches LGPE's usable balls. If you don't know how GO->LGPE IVs work, you probably don't wanna mess with them.
Since GO legality is complicated and tedious, once you make a legal Meltan and Melmetal, don't make anything else that originated from GO.
That would probably save you a lot of headache. :3