As of New year 2018, WonderSwan will now be using Libretro API for save data handling. For most cases, old save file should be compatible. Make a copy of your existing WonderSwan .sav files, and rename them to .srm(keep the original filename).
On a similar note, the core now supports softpatching… just refer to the patch’s readme for rom details required and just place the .ips/.bps file to where your rom is and rename it exactly as the filename of the rom you want to patch.
e.g.
rom filename ====> ips filename
Rockman EXE WS (Japan).zip = Rockman EXE WS (Japan).ips
Rockman EXE WS (Japan).ws = Rockman EXE WS (Japan).ips