Kaphotics

You must have a modified Nintendo switch with custom firmware installed first, otherwise you will not be able to access your save data.

As was mentioned above, use PKHeX to unlock/add the event items. Manaphy is shiny locked.

No, this program does not support adding NPC, nor does it support editing scripts.

It's nonsense randomness. Open a valid save file in a hex editor and scroll through it, and do the same for yours. Even without knowing what it should be, you'll be able to tell that the data is not what it should be.

Not documented; not really worth when you'll unlock them all by just playing the game.

Open it in a hex editor and compare it to other saves. What you uploaded is entirely junk and nothing can be recovered.

Probably not restoring it to your cartridge correctly. Save data doesn't magically revert, it only stores what it has available, and RBY have no backup save file functionality, so any changes visible in PKHeX should be visible once correctly restored.

PKHeX has a setting you can enable to turn on backwards conversion, but it isn't perfect. You'd have to manually add the information that was lost during transfer (such as 3DS origin info).

Since you modified one of the immutable values, HOME will know and will reject it if you try to move it back in. PKHeX does not know the HOME upload data, it only has the data from the sav/PKM. You can try manually transferring it back to Gen7 and then retry transferring to HOME until you get a satisfactory value, but that's something that HOME can potentially detect in the future (importing same values).

string buffers are allocated and reused, meaning that the previous usage of that memory may have had data (not zeroes). renaming a pokemon does not clear the buffer, so longer nicknames will remain hidden underneath the new nickname & terminator. for generation 4+ encounters, you are fine grabbing from the database without modification; gens 1-3 do have trash bytes that are poorly understood, but don't matter when transferred to recent games (cleared/reset).

Latest development build of PKHeX has a setting that you can turn on to retain the met date for 4->5 transfers.

It means it failed to validate the encounter slot RNG correlation, which likely means it's not legal. The severity of the check is currently Fishy for Gen3 as vblanks may cause it to be disjointed, but in 99% of cases it's a correct assessment. How to remove it? Only assign PIDIV spreads that the encounter slot can have. Use a tool like Pokefinder to search.

Likely not; verify you installed the required runtime: https://learn.microsoft.com/en-us/dotnet/core/install/how-to-detect-installed-versions?pivots=os-windows

So, how to "fix" it? To start, I rearranged the 0x1000-sized blocks in sequential order (based on their offset 0x0FF4 value); since blocks 5+ are for box data storage, I can "copy" block 7 and re-label it as block 8; sure the data might be corrupt, but it's better than an entirely missing block. Probably wasn't anything lost, because now that the save file opens in PKHeX (and emulators/cart) it seems you didn't store anything besides boxes 1/2 and 14. POKEMON SAPP_AXPE-0.sav

Referencing the structure of Gen3 saves, your save file is missing necessary blocks and has duplicate blocks. Missing: Block 08 Normally, the save file is 14 blocks for a primary/backup, and another set for the other save. This one is a little all over the place, probably because blockwise writing failed once and it never saved the primary/backup sets completely (only one full set, kinda).