The file is full of garbage, no real save data inside.
Besides that the proper size for Gen 3 saves is 128kb. You should check if FlashGBX is able to dump the full 128kb save.
He provided ME3 files for them on his Github https://github.com/notblisy/RUBYSAPPHIREDLC/tree/main/MYSTERY EVENT 3 EVENTS
Use the WC3 Plugin to inject them into your save.
No, you can still use the file and you don't have to delete anything.
Your .nds file can not just disappear after using PKHeX. PKHeX does not remove or delete files. It still has to be somewhere.