Kaphotics

The game uses the value to pivot between preprogrammed Trainer Teams. It doesn't use the species value directly. If you wish to change Trainer Team data, that's only possible via ROM edits, not save file edits.

If it reached you via bot trade, then it should be obvious why it reset friendship when reaching you. The middleman (bot) has to have a friendship value. When it trades to you, you become the newest handler, and the previous handler's friendship is overwritten with the new friendship value for you, which is the default friendship minimum on trade. How to fix it? Either be the OT of the Pokemon, or inject it directly to your save file without a bot. Or raise the friendship after receiving it, like everyone else who isn't cheating.

Did it originate from an encounter that is allowed to have marks? Things like gifts and raids/ fixed single encounters cannot be found with marks.

Use the encounter database, especially if you don't know how to fabricate data perfectly from scratch. Celebi can only be obtained in Crystal for Virtual Console games, which your save file is a cartridge game (not Virtual Console). Your save file has more than a few impossible movesets (Extremespeed Raikou). The legality checker is flagging your hacks as intended. "Unable to match an encounter" means exactly what it says -- if you have a Wild Level 2 Mew, that's not a legitimate encounter. How is it supposed to find something it matches if there isn't anything it matches? And how would it be able to fix something that is impossible to have? The program is not going to brute force which property/properties are invalid and tweak them accordingly. Distill the issue to what you're wanting the end result to be -- species, moves. Then use the encounter database to start with something that can eventually have that result. Then update the Pokémon to the state you want it to be, without making it illegal.

Starting in generation 6, Pokemon store a friendship value for the original trainer, and a separate friendship value for the trainer that last had possession of it. When you trade it to a new trainer, that new trainer has not built up any friendship, so it will be at whatever the minimum is (usually 70 for trades). Since you've not provided any specifics, I can only assume that you're looking at the current handler friendship value, after it was traded.

Does not apply to eggs, otherwise PKHeX would be flagging it.

If it already passed through HOME, then it cannot be changed legally. An entirely different pokemon would have to be transferred instead, unless you try transferring an untransferred clone (which isn't really legal, but HOME doesn't really check).

Read the first post. You don't. You transfer them legitimately from their original game.

Refer to the save file structure on bulbapedia; the save file needs to have the correct layout of 0x1000 chunks of save blocks. Using a hex editor, you can find the correct blocks of save data and reassemble a working save file. 005 Pokemon Leaf Green.srm

Check the error log file next to the exe file.

pkNX outputs a folder of all modified files for a given ROM you open. This output folder is what is copied to the console to use as the layeredfs file replacements. You have a set of layeredfs file replacements from someone else that you wish to modify. So, you do the process in reverse. You put the layeredfs file replacements back into pkNX's output folder. When you open the ROM to edit, pkNX will find those replacements as if the program was the one that originally put them there.

No, you put the mod files in pkNX's output folder, as if they were modified by you.

Put the files you wish to have modified in pknx's output folder, and pkNX will read those when you open your ROM as usual. The program checks the output folder first, so any modified files will be used if available.

Obtaining TID/SID for games. For encounters that originate from Violet, they should have Violet trainer data, and not reuse the Scarlet trainer data (with a changed Version value). To obtain an encounter from a given Version, you should have trainer data available for that Version. Otherwise ALM will fabricate it by reusing TID/SID and changing Version. Reusing trainer data is not legal. Correct.

Please think about it. As was mentioned to you in your thread, data which has already touched HOME should not have immutable values changed. They check the immutable data against the tracker, and reject (error 10015) it from re-entering HOME. Anyone can try to upload your tampered data, and will be rejected as well, so you won't be fooling anyone.