Not sure if this'll work (it worked the other way round 512kb to 1Mb) but ...
(Always make a backup in case things go wrong):
> Create a new save file by running game (hopefully this will be a 'blank' 512kMb save file)
- or alternatively use a copy of an old SAV file that you know IS 512kb in size
> Using a Hex editor (I use HxDen for this) load BOTH your old 1mb sav and the New 512kb file
(You'll end up with 2 tabs, each with a save file code in)
> Select the old 1mb tab & select the first 512kb of the code & 'copy' it
> Select the new 512kb tab & after making sure you're at the very start of the file - Use 'Paste/Write'
(all of the code will turn red to show that it's been overwritten)
> Saved this newly modified file, copy it back to your flashcart & try it out
let us know if this works