Emerald.fla - bad ROM dump
Emerald(different).sav - only has blocks 8-13,0,1. Blocks 2-7 are missing.
By taking another save file and transplanting the blocks you have into it, then opening in PKHeX:
Your party and some of your trainer data is stored in blocks 0 and 1, but blocks 8-13 in your save file (latter half of your boxes) were empty. So, if you had anything in your boxes it's gone; it's now whatever was in the donor save file (Twitch Plays Pokémon E merald).
donor emerald.sav