Poke J

The journal only comes up if the game detects that the last time you played was over 24 hours ago. I know you are soft resetting, but what was the last day you saved the game on? Was it over 24 hours ago? Try saving the game again and see if that fixes the problem. If it does fix the problem make sure you resave the game at the start of each reset session so the journal will not come up.

1) Manaphy 2) Zoroark 3) Espeon

To get Lillie's Clefairy you will have to dump the RAM of the game during a battle when Clefairy is on the field. That way you have the chance to preserve data such as ID and SID that a code would discard (also considering the fact you don't battle Clefairy directly). However, you would probably need to run it on an emulator since I don't think there are any tools that can dump a hacked 3DS RAM. The Ribombee and Comfey you can easily extract by doing a multi battle with Lillie as your partner then save the battle video. Then dump the battle video and open it in PKHeX, however; if I remember correctly parts of the data for Pokemon encountered in the Battle Tree changes every time you do a new challenge and that will require you to hack your 3DS if it isn't already hacked. One thing I have learnt from dumping trainers Pokemon from past gens is that every Pokemon on the trainers team usually has a different ID and SID since NPCs don't get assigned a strict ID and SID combo from what I can tell. So using the data from the Lillie's Vulpix event will probably not be the same.

I'm not to familiar with PokeFinder, but does it give you the option to find a Method 1 spread? If you can search PIDs using Method 1 use that since the Lapras that you get in Silph Co. uses Method 1.

I've looked at it and as long as there isn't some factor at play that I am unaware of, I believe that this is an error on PKHeX's part.

In terms of your Safari Ball question only Pokémon that can be caught in a Safari Zone that you had to pay money to get into can be in Safari Balls. Therefore, anyone of those Pokémon can pass the ball down to their offspring. However, ball inheritance will always take the mother’s ball (excluding Cherish Ball and Master Ball) if the father isn’t the same species as the mother. If it is a male and Ditto combo breeding the male’s ball will be passed down. In the case that both Pokémon are the same species both parents can pass down the ball. If you need more information on what Pokémon can be in which ball please look at the provided link. https://www.serebii.net/games/pokeball.shtml

@LoganG I believe I've found the issue. It seems that your file path isn't correct. Every time I made a same file path as you it would corrupt the save so to fix that make another folder inside your Omega Ruby folder and place the main file in there. You can give the folder whatever name you want.

Sorry for the delay. Can you tell me if your file looks just like mine (red rectangle) and if your file path looks similar to mine (green rectangle) ignore the last part of my file path "current" since that is only how I labeled that save.

Try removing the .sav from the file name and leave the file named main.

It doesn’t matter where the files from, I need to know if the folder on your SD card that you put the save in if there are any other files in that folder.

Is there any other files besides the main in the folder that you are importing the save from?

@Helmschrot it seems the legality check didn't work properly since these Pokemon are not legal. Those starters can't be in any ball besides the standard Poke Ball.

@droidpersonif you just want a Pokemon with the hidden ability I could breed you a Litten with Intimidate. However, the Galar starters don't have their hidden abilities released yet so you'll have to wait for those ones to become possible.

@javisoto99it appears to be an error with the current version of PKHeX. I was able to replicate the issue multiple times with Ralts that I hatched in the Battle Frontier. For some reason PKHeX is detecting that the Battle Frontier is a Platinum only location and if the egg met conditions is changed to Link Trade (Egg) it will turn legal.

By chance could you upload the file here? It'll make it easier to determine the issue.