I'd assume that you're using a downloaded version patch; patches contain a replacement exefs -- your edited exefs content is being replaced with the patch's data.
DeSmuME plays gen4/gen5 games.
PKHeX does not support loading of past gen gift files, as they are not convertible. Gift files (wondercards / pgf/pgt) are templates which the game has to generate itself.
csv is a Comma Separated Value file, which only stores text.
Can't store images in a .csv; writing a .xls would require adding some .dll's which I'd rather not.
Feed them save files; ramsavs are not supported in the current release but are if you compile the source - next version that is posted will support ramsavs.
It'll just tell you what flags were set/unset based on the before/after input.
Before the gender changing was disabled, people would have games crash/lock up because it isn't a simple bit flip in the save file (although the indicator that PKHeX reads is totally valid).
The overworld data (such as models and sprites) loaded is likely the culprit in preventing the switch; although, there's probably some other gender-specific data in the save too.
All of our savedata notes are on this site's wiki and in PKHeX's source code.
for the record I don't even own a 3ds &/ xyoras so I can't research if stuff can be changed -- which pretty much leaves it up to the users to figure out / suggest new stuff that is feasible. Hard stuff which isn't already understood will never really happen; gender changing isn't easily deducible and offers very little gain compared to time spent :\
9.2 firmware or below 3DS (not new3DS) (to run exploits)
Gateway 3DS Flashcart (to run the hacked game on emunand)
Windows machine (to run the existing hack programs on this forum)
As with all minor in-game edits (not program function/utility), it is left to the community to research what they want -- I only implement editing into the program after it is clear what has to be changed in the files. I'm only one person, and there's many other things that I should be doing with my time.
As Timeboy already suggested, do a flag diff to see what flags you have to switch to replay the event story.
Yes I deleted it; Battle Boxes are used by official tournaments and should not be tampered with. You can always move stuff into them in-game when it is not locked.
Can always restart the program, or you can just make all of your edits off the existing data. If you clear it you still have to enter the data anyway.
I'll likely add a feature to load empty data by viewing an empty slot, if that doesn't exist already.